Histone Deacetylase and Tubulin Deacetylase Inhibitors

ABSTRACT

In recognition of the need to develop novel therapeutic agents and efficient methods for the synthesis thereof, the present invention provides novel inhibitors of histone deacetylases, tubulin deacetylases, and/or aggresome inhibitors, and pharmaceutically acceptable salts and derivatives thereof. The inventive compounds fall into two classes—“isotubacin” class and “isoisotubacin” class—all of which include a 1,3-dioxane core. The present invention further provides methods for treating disorders regulated by histone deacetylase activity, tubulin deacetylase activity, and/or the aggresome (e.g., proliferative diseases, cancer, inflammatory diseases, protozoal infections, protein degradation disorders, protein deposition disorders, etc.) comprising administering a therapeutically effective amount of an inventive compound to a subject in need thereof. The present invention also provides methods for preparing compounds of the invention.

RELATED APPLICATIONS

The present application claims priority under 35 U.S.C. § 119(e) to U.S.provisional patent application, U.S. Ser. No. 60/797,211, filed May 3,2006; which is incorporated herein by reference.

GOVERNMENT SUPPORT

The work described herein was supported, in part, by grants from theNational Institutes of Health (370 31215 017490 614101 0001 00000; 37031215 133800 341450 0402 44046). The United States government may havecertain rights in the invention.

BACKGROUND OF THE INVENTION

The identification of small organic molecules that affect specificbiological functions is an endeavor that impacts both biology andmedicine. Such molecules are useful as therapeutic agents and as probesof biological function. In but one example from the emerging field ofchemical genetics, in which small molecules can be used to alter thefunction of biological molecules to which they bind, these moleculeshave been useful at elucidating signal transduction pathways by actingas chemical protein knockouts, thereby causing a loss of proteinfunction. (Schreiber et al., J. Am. Chem. Soc., 1990, 112, 5583;Mitchison, Chem. and Biol., 1994, 1, 3) Additionally, due to theinteraction of these small molecules with particular biological targetsand their ability to affect specific biological function (e.g. genetranscription), they may also serve as candidates for the development ofnew therapeutics. One important class of small molecules, naturalproducts, which are small molecules obtained from nature, clearly haveplayed an important role in the development of biology and medicine,serving as pharmaceutical leads, drugs (Newman et al., Nat. Prod. Rep.2000, 17, 215-234), and powerful reagents for studying cell biology(Schreiber, S. L. Chem. and Eng. News 1992 (October 26), 22-32).

One biological target of recent interest is histone deacetylase (see,for example, a discussion of the use of inhibitors of histonedeacetylases for the treatment of cancer: Marks et al. Nature ReviewsCancer 2001, 1, 194; Johnstone et al. Nature Reviews Drug Discovery2002, 1, 287). Post-translational modification of proteins throughacetylation and deacetylation of lysine residues plays a critical rolein regulating their cellular functions. HDACs are zinc hydrolases thatmodulate gene expression through deacetylation of the N-acetyl-lysineresidues of histone proteins and other transcriptional regulators(Hassig et al. Curr. Opin. Chem. Biol. 1997, 1, 300-308). HDACsparticipate in cellular pathways that control cell shape anddifferentiation, and an HDAC inhibitor has been shown effective intreating an otherwise recalcitrant cancer (Warrell et al. J. Natl.Cancer Inst. 1998, 90, 1621-1625). At this time, eleven human HDACs,which use Zn as a cofactor, have been identified (Taunton et al. Science1996, 272, 408-411; Yang et al. J. Biol. Chem. 1997, 272, 28001-28007.Grozinger et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 4868-4873; Kaoet al. Genes Dev. 2000, 14, 55-66. Hu et al. J. Biol. Chem. 2000, 275,15254-15264; Zhou et al. Proc. Natl. Acad. Sci. U.S.A. 2001, 98,10572-10577; Venter et al. Science 2001, 291, 1304-1351) these membersfall into three classes (class I, II, and IV). An additional seven HDACshave been identified which use NAD as a cofactor. To date, no smallmolecules are known that selectively target any particular class orindividual members of this family ((for example ortholog-selective HDACinhibitors have been reported: (a) Meinke et al. J. Med. Chem. 2000, 14,4919-4922; (b) Meinke, et al. Curr. Med. Chem. 2001, 8, 211-235). Thereremains a need for preparing structurally diverse HDAC and tubulindeacetylase (TDAC) inhibitors particularly ones that are potent and/orselective inhibitors of particular classes of HDACs or TDACs andindividual HDACs and TDACs.

SUMMARY OF THE INVENTION

The present invention provides novel histone deacetylase and tubulindeacetylase inhibitors and methods of preparing and using thesecompounds. These compounds are particularly useful in the treatment ofproliferative diseases such as cancer, inflammatory diseases, infectiousdiseases, protein degradation disorders, and protein depositiondisorders such as Alzheimer's Disease. Certain compounds areparticularly useful in specifically inhibiting one class or member ofHDACs. Other compounds are particularly useful in specificallyinhibiting one class or member of tubulin deacetylases (TDAC). Yet othercompounds are useful in inhibiting degradation of proteins by theaggresome.

The present invention provides novel inhibitors of HDACs and TDACs witha 1,3-dioxane core structure. Compounds of the invention basically fallinto two classes, wherein the 1,3-dioxane core of the compound isoriented differently in each class. That is, the 1,3-dioxane core isrotated 1200 in each class as compared to tubacin derivatives and asshown in the structures below (see, also, FIG. 1). The inventivecompounds are of the formulae:

wherein

R₁ is cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(A); —C(═O)R_(A); —CO₂R_(A); —SR_(A); —SOR_(A);—SO₂R_(A); —N(R_(A))₂; —NHC(O)R_(A); or —C(R_(A))₃; wherein eachoccurrence of R_(B) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety;

R₂ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(B); —C(═O)R_(B);—CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂;—NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; and

R₃ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(C); —C(═O)R_(C);—CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N(R_(C))₂;—NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; andpharmaceutically acceptable salts and derivatives thereof. In general,R₁ comprises a metal chelating functional group (e.g., hydroxyamicacids, thiols, carboxic acids, ortho-aminoanilides, etc.). The metalchelating group is thought to bind the active site Zn⁺² ion ofdeacetylase enzymes. In certain embodiments, R₂ is a substituted orunsubstituted heteroaliphatic moiety (e.g., a heteroaliphatic moietysubstituted with a heteroaryl ring, which may be optionallysubstituted). In certain embodiments, R₃ is a substituted orunsubstituted aromatic ring system (e.g., a substituted or unsubstitutedphenyl).

Compounds of formula:

that is, tubacin derivatives, have been described in U.S. patentapplications, U.S. Ser. No. 11/386,959, filed Mar. 22, 2006; U.S. Ser.No. 60/664,470, filed Mar. 22, 2005; U.S. Ser. No. 60/289,850, filed May9, 2001; U.S. Ser. No. 10/144,316, filed May 9, 2002; and U.S. Ser. No.10/621,276, filed Jul. 17, 2003; each of which is incorporated herein byreference. These compounds have been found to be particularly useful ininhibiting HDACs such as HDAC6 and also in the treatment of multiplemyeloma by inhibiting HDAC6 known to play a role in the degradation ofproteins by the aggresome.

Inventive compounds of the class of formula:

are compounds of the “isotubacin” class. The 1,3-dioxane core of thesecompounds has been rotated 120° counter-clockwise as compared tocompounds of the “tubacin” class. The compounds of this class are alsouseful in treating cancer (e.g., multiple myeloma, breast cancer,non-Hodgkin's lymphoma, ovarian cancer, acute myelogenous leukemia),protein degradation disorders (e.g., multiple myeloma, neurodegenerativedisorders), protein deposition disorders (e.g., neurogenerativedisorders), infectious diseases, and proliferative disorders (e.g.,diabetic retinopathy, inflammatory diseases, angiogenesis).Pharmaceutical compositions and kits comprising these compounds are alsoprovided by the present invention. In certain particular embodiments,compounds of this class are useful in the treatment of multiple myeloma,leukemia, lymphoma, breast cancer, and prostate cancer. Pharmaceuticalcomposition of the inventive compounds may also comprises otherchemotherapeutic agents or other pharmaceutical agents typicallyadministered during the treatment of cancer (e.g., anti-nauseamedications, analgesics, nutritional supplements, etc.). The presentinvention also provides synthetic method for preparing compounds of the“isotubacin” class.

Inventive compounds of the class of formula:

are compounds of the “isoisotubacin” class. The 1,3-dioxane core of thecompounds of this class has been rotated 120° clockwise as compared tocompounds of the “tubacin” class. The compounds of this class are alsouseful in treating cancer (e.g., multiple myeloma, breast cancer,non-Hodgkin's lymphoma, ovarian cancer, acute myelogenous leukemia),protein degradation disorders (e.g., neurodegenerative disorders,multiple myeloma), protein deposition disorders (e.g., neurodegenerativedisorders), infectious diseases, and proliferative disorders (e.g.,diabetic retinopathy, inflammatory diseases, angiogenesis).Pharmaceutical compositions and kits comprising these compounds are alsoincluded. In certain particular embodiments, compounds of this class areuseful in the treatment of multiple myeloma, leukemia, lymphoma, breastcancer, and prostate cancer. Pharmaceutical composition of the inventivecompounds may also comprises other chemotherapeutic agents or otherpharmaceutical agents typically administered during the treatment ofcancer (e.g., anti-nausea medications, analgesics, nutritionalsupplements, etc.). The present invention also provides synthetic methodfor preparing compounds of the “isoisotubacin” class.

The inventive compounds are also useful as tools to probe biologicalfunction (e.g., the degradation of proteins by the aggresome; inhibitionof histone deacetylases, inhibition of tubulin deacetylases). Forexample, the compounds may be administered to wild type cells or alteredcells to understand protein degradation pathways or the effect ofacetylation on a protein's function. In certain embodiments, thecompound inhibits a specific histone or tubulin deacetylase. Thecompounds may also be used to elucidate the cell cycle.

In another aspect, the present invention provides methods for inhibitinghistone deacetylase activity, tubulin deacetylase activity, or aggresomeactivity in a patient or a biological sample, comprising administeringto the patient, or contacting the biological sample with an effectiveamount of an inventive compound or a pharmaceutical composition thereof.

DEFINITIONS

Certain compounds of the present invention, and definitions of specificfunctional groups are also described in more detail below. For purposesof this invention, the chemical elements are identified in accordancewith the Periodic Table of the Elements, CAS version, Handbook ofChemistry and Physics, 75^(th) Ed., inside cover, and specificfunctional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in “OrganicChemistry”, Thomas Sorrell, University Science Books, Sausalito: 1999,the entire contents of which are incorporated herein by reference.Furthermore, it will be appreciated by one of ordinary skill in the artthat the synthetic methods, as described herein, utilize a variety ofprotecting groups.

It will be appreciated that the compounds, as described herein, may besubstituted with any number of substituents or functional moieties. Ingeneral, the term “substituted” whether preceded by the term“optionally” or not, and substituents contained in formulas of thisinvention, refer to the replacement of hydrogen radicals in a givenstructure with the radical of a specified substituent. When more thanone position in any given structure may be substituted with more thanone substituent selected from a specified group, the substituent may beeither the same or different at every position. As used herein, the term“substituted” is contemplated to include all permissible substituents oforganic compounds. In a broad aspect, the permissible substituentsinclude acyclic and cyclic, branched and unbranched, carbocyclic andheterocyclic, aromatic and nonaromatic substituents of organiccompounds. For purposes of this invention, heteroatoms such as nitrogenmay have hydrogen substituents and/or any permissible substituents oforganic compounds described herein which satisfy the valencies of theheteroatoms. Furthermore, this invention is not intended to be limitedin any manner by the permissible substituents of organic compounds.Combinations of substituents and variables envisioned by this inventionare preferably those that result in the formation of stable compoundsuseful in the treatment, for example of proliferative disorders,including, but not limited to cancer. The term “stable”, as used herein,preferably refers to compounds which possess stability sufficient toallow manufacture and which maintain the integrity of the compound for asufficient period of time to be detected and preferably for a sufficientperiod of time to be useful for the purposes detailed herein.

The term “acyl”, as used herein, refers to a carbonyl-containingfunctionality, e.g., —C(═O)R′, wherein R′ is an aliphatic, alycyclic,heteroaliphatic, heterocyclic, aryl, heteroaryl, (aliphatic)aryl,(heteroaliphatic)aryl, heteroaliphatic(aryl) orheteroaliphatic(heteroaryl) moiety, whereby each of the aliphatic,heteroaliphatic, aryl, or heteroaryl moieties is substituted orunsubstituted, or is a substituted (e.g., hydrogen or aliphatic,heteroaliphatic, aryl, or heteroaryl moieties) oxygen or nitrogencontaining functionality (e.g., forming a carboxylic acid, ester, oramide functionality).

The term “aliphatic”, as used herein, includes both saturated andunsaturated, straight chain (i.e., unbranched) or branched aliphatichydrocarbons, which are optionally substituted with one or morefunctional groups. As will be appreciated by one of ordinary skill inthe art, “aliphatic” is intended herein to include, but is not limitedto, alkyl, alkenyl, alkynyl moieties. Thus, as used herein, the term“alkyl” includes straight and branched alkyl groups. An analogousconvention applies to other generic terms such as “alkenyl”, “alkynyl”and the like. Furthermore, as used herein, the terms “alkyl”, “alkenyl”,“alkynyl” and the like encompass both substituted and unsubstitutedgroups. In certain embodiments, as used herein, “lower alkyl” is used toindicate those alkyl groups (substituted, unsubstituted, branched orunbranched) having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl and alkynyl groups employedin the invention contain 1-20 aliphatic carbon atoms. In certain otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in theinvention contain 1-10 aliphatic carbon atoms. In yet other embodiments,the alkyl, alkenyl, and alkynyl groups employed in the invention contain1-8 aliphatic carbon atoms. In still other embodiments, the alkyl,alkenyl, and alkynyl groups employed in the invention contain 1-6aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl,and alkynyl groups employed in the invention contain 1-4 carbon atoms.Illustrative aliphatic groups thus include, but are not limited to, forexample, methyl, ethyl, n-propyl, isopropyl, allyl, n-butyl, sec-butyl,isobutyl, tert-butyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl,n-hexyl, sec-hexyl, moieties and the like, which again, may bear one ormore substituents. Alkenyl groups include, but are not limited to, forexample, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and thelike. Representative alkynyl groups include, but are not limited to,ethynyl, 2-propynyl (propargyl), 1-propynyl and the like.

The term “alicyclic”, as used herein, refers to compounds which combinethe properties of aliphatic and cyclic compounds and include but are notlimited to cyclic, or polycyclic aliphatic hydrocarbons and bridgedcycloalkyl compounds, which are optionally substituted with one or morefunctional groups. As will be appreciated by one of ordinary skill inthe art, “alicyclic” is intended herein to include, but is not limitedto, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties, which areoptionally substituted with one or more functional groups. Illustrativealicyclic groups thus include, but are not limited to, for example,cyclopropyl, —CH₂-cyclopropyl, cyclobutyl, —CH₂-cyclobutyl, cyclopentyl,—CH₂-cyclopentyl-n, cyclohexyl, —CH₂-cyclohexyl, cyclohexenylethyl,cyclohexanylethyl, norbornyl moieties and the like, which again, maybear one or more substituents.

The term “alkoxy” (or “alkyloxy”), or “thioalkyl” as used herein refersto an alkyl group, as previously defined, attached to the parentmolecular moiety through an oxygen atom or through a sulfur atom. Incertain embodiments, the alkyl group contains 1-20 aliphatic carbonatoms. In certain other embodiments, the alkyl group contains 1-10aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl,and alkynyl groups employed in the invention contain 1-8 aliphaticcarbon atoms. In still other embodiments, the alkyl group contains 1-6aliphatic carbon atoms. In yet other embodiments, the alkyl groupcontains 1-4 aliphatic carbon atoms. Examples of alkoxy, include but arenot limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy,tert-butoxy, neopentoxy and n-hexoxy. Examples of thioalkyl include, butare not limited to, methylthio, ethylthio, propylthio, isopropylthio,n-butylthio, and the like.

The term “alkylamino” refers to a group having the structure —NHR′wherein R′ is alkyl, as defined herein. The term “aminoalkyl” refers toa group having the structure NH₂R′—, wherein R′ is alkyl, as definedherein. In certain embodiments, the alkyl group contains 1-20 aliphaticcarbon atoms. In certain other embodiments, the alkyl group contains1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl,alkenyl, and alkynyl groups employed in the invention contain 1-8aliphatic carbon atoms. In still other embodiments, the alkyl groupcontains 1-6 aliphatic carbon atoms. In yet other embodiments, the alkylgroup contains 1-4 aliphatic carbon atoms. Examples of alkylaminoinclude, but are not limited to, methylamino, ethylamino,iso-propylamino and the like.

Some examples of substituents of the above-described aliphatic (andother) moieties of compounds of the invention include, but are notlimited to aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl;alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy;alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH;—NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂;—CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x);—OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x)wherein each occurrence of R_(x) independently includes, but is notlimited to, aliphatic, alycyclic, heteroaliphatic, heterocyclic, aryl,heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic,heteroaliphatic, alkylaryl, or alkylheteroaryl substituents describedabove and herein may be substituted or unsubstituted, branched orunbranched, cyclic or acyclic, and wherein any of the aryl or heteroarylsubstituents described above and herein may be substituted orunsubstituted. Additional examples of generally applicable substituentsare illustrated by the specific embodiments shown in the Examples thatare described herein.

In general, the term “aryl”, as used herein, refers to a stable mono- orpolycyclic, unsaturated moiety having preferably 3-14 carbon atoms, eachof which may be substituted or unsubstituted. In certain embodiments,the term “aryl” refers to a planar ring having p-orbitals perpendicularto the plane of the ring at each ring atom and satisfying the Huckelrule where the number of pi electrons in the ring is (4n+2) wherein n isan integer. A mono- or polycyclic, unsaturated moiety that does notsatisfy one or all of these criteria for aromaticity is defined hereinas “non-aromatic”, and is encompassed by the term “alicyclic”.

In general, the term “heteroaryl”, as used herein, refers to a stablemono- or polycyclic, unsaturated moiety having preferably 3-14 carbonatoms, each of which may be substituted or unsubstituted; and comprisingat least one heteroatom selected from O, S and N within the ring (i.e.,in place of a ring carbon atom). In certain embodiments, the term“heteroaryl” refers to a planar ring comprising at least one heteroatom,having p-orbitals perpendicular to the plane of the ring at each ringatom, and satisfying the Huckel rule where the number of pi electrons inthe ring is (4n+2) wherein n is an integer.

It will also be appreciated that aryl and heteroaryl moieties, asdefined herein may be attached via an alkyl or heteroalkyl moiety andthus also include -(alkyl)aryl, -(heteroalkyl)aryl,-(heteroalkyl)heteroaryl, and -(heteroalkyl)heteroaryl moieties. Thus,as used herein, the phrases “aryl or heteroaryl moieties” and “aryl,heteroaryl, -(alkyl)aryl, -(heteroalkyl)aryl, -(heteroalkyl)heteroaryl,and -(heteroalkyl)heteroaryl” are interchangeable. Substituents include,but are not limited to, any of the previously mentioned substituents,i.e., the substituents recited for aliphatic moieties, or for othermoieties as disclosed herein, resulting in the formation of a stablecompound.

The term “aryl”, as used herein, does not differ significantly from thecommon meaning of the term in the art, and refers to an unsaturatedcyclic moiety comprising at least one aromatic ring. In certainembodiments, “aryl” refers to a mono- or bicyclic carbocyclic ringsystem having one or two aromatic rings including, but not limited to,phenyl, naphthyl, tetrahydronaphthyl, indanyl, indenyl and the like.

The term “heteroaryl”, as used herein, does not differ significantlyfrom the common meaning of the term in the art, and refers to a cyclicaromatic radical having from five to ten ring atoms of which one ringatom is selected from S, O and N; zero, one or two ring atoms areadditional heteroatoms independently selected from S, O and N; and theremaining ring atoms are carbon, the radical being joined to the rest ofthe molecule via any of the ring atoms, such as, for example, pyridyl,pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl,oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl,quinolinyl, isoquinolinyl, and the like.

It will be appreciated that aryl and heteroaryl groups (includingbicyclic aryl groups) can be unsubstituted or substituted, whereinsubstitution includes replacement of one or more of the hydrogen atomsthereon independently with any one or more of the following moietiesincluding, but not limited to: aliphatic; alicyclic; heteroaliphatic;heterocyclic; aromatic; heteroaromatic; aryl; heteroaryl; alkylaryl;heteroalkylaryl; alkylheteroaryl; heteroalkylheteroaryl; alkoxy;aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio;heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃;—CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x);—CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂;—N(R_(x))₂; —S(O)R_(x); —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein eachoccurrence of R_(x) independently includes, but is not limited to,aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic,heteroaromatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl,heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic,alicyclic, heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroarylsubstituents described above and herein may be substituted orunsubstituted, branched or unbranched, saturated or unsaturated, andwherein any of the aromatic, heteroaromatic, aryl, heteroaryl,-(alkyl)aryl or -(alkyl)heteroaryl substituents described above andherein may be substituted or unsubstituted. Additionally, it will beappreciated, that any two adjacent groups taken together may represent a4, 5, 6, or 7-membered substituted or unsubstituted alicyclic orheterocyclic moiety. Additional examples of generally applicablesubstituents are illustrated by the specific embodiments shown in theExamples that are described herein.

The term “cycloalkyl”, as used herein, refers specifically to groupshaving three to seven, preferably three to ten carbon atoms. Suitablecycloalkyls include, but are not limited to cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, cycloheptyl and the like, which, as in the caseof aliphatic, alicyclic, heteroaliphatic or heterocyclic moieties, mayoptionally be substituted with substituents including, but not limitedto aliphatic; alicyclic; heteroaliphatic; heterocyclic; aromatic;heteroaromatic; aryl; heteroaryl; alkylaryl; heteroalkylaryl;alkylheteroaryl; heteroalkylheteroaryl; alkoxy; aryloxy; heteroalkoxy;heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F;Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH;—CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x);—OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x)wherein each occurrence of R_(x) independently includes, but is notlimited to, aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl,heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic,alicyclic, heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroarylsubstituents described above and herein may be substituted orunsubstituted, branched or unbranched, saturated or unsaturated, andwherein any of the aromatic, heteroaromatic, aryl or heteroarylsubstituents described above and herein may be substituted orunsubstituted. Additional examples of generally applicable substituentsare illustrated by the specific embodiments shown in the Examples thatare described herein.

The term “heteroaliphatic”, as used herein, refers to aliphatic moietiesin which one or more carbon atoms in the main chain have beensubstituted with a heteroatom. Thus, a heteroaliphatic group refers toan aliphatic chain which contains one or more oxygen, sulfur, nitrogen,phosphorus or silicon atoms, e.g., in place of carbon atoms.Heteroaliphatic moieties may be linear or branched, and saturated orunsaturated. In certain embodiments, heteroaliphatic moieties aresubstituted by independent replacement of one or more of the hydrogenatoms thereon with one or more moieties including, but not limited toaliphatic; alicyclic; heteroaliphatic; heterocyclic; aromatic;heteroaromatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy;aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio;heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃;—CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x);—CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂;—N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence ofR_(x) independently includes, but is not limited to, aliphatic,alicyclic, heteroaliphatic, heterocyclic, aromatic, heteroaromatic,aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl orheteroalkylheteroaryl, wherein any of the aliphatic, alicyclic,heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroarylsubstituents described above and herein may be substituted orunsubstituted, branched or unbranched, saturated or unsaturated, andwherein any of the aromatic, heteroaromatic, aryl or heteroarylsubstituents described above and herein may be substituted orunsubstituted. Additional examples of generally applicable substituentsare illustrated by the specific embodiments shown in the Examples thatare described herein.

The term “heterocycloalkyl”, “heterocycle” or “heterocyclic”, as usedherein, refers to compounds which combine the properties ofheteroaliphatic and cyclic compounds and include, but are not limitedto, saturated and unsaturated mono- or polycyclic cyclic ring systemshaving 5-16 atoms wherein at least one ring atom is a heteroatomselected from O, S and N (wherein the nitrogen and sulfur heteroatomsmay be optionally be oxidized), wherein the ring systems are optionallysubstituted with one or more functional groups, as defined herein. Incertain embodiments, the term “heterocycloalkyl”, “heterocycle” or“heterocyclic” refers to a non-aromatic 5-, 6- or 7-membered ring or apolycyclic group wherein at least one ring atom is a heteroatom selectedfrom O, S and N (wherein the nitrogen and sulfur heteroatoms may beoptionally be oxidized), including, but not limited to, a bi- ortri-cyclic group, comprising fused six-membered rings having between oneand three heteroatoms independently selected from oxygen, sulfur andnitrogen, wherein (i) each 5-membered ring has 0 to 2 double bonds, each6-membered ring has 0 to 2 double bonds and each 7-membered ring has 0to 3 double bonds, (ii) the nitrogen and sulfur heteroatoms may beoptionally be oxidized, (iii) the nitrogen heteroatom may optionally bequaternized, and (iv) any of the above heterocyclic rings may be fusedto an aryl or heteroaryl ring. Representative heterocycles include, butare not limited to, heterocycles such as furanyl, thiofuranyl, pyranyl,pyrrolyl, thienyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl,imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolyl,oxazolidinyl, isooxazolyl, isoxazolidinyl, dioxazolyl, thiadiazolyl,oxadiazolyl, tetrazolyl, triazolyl, thiatriazolyl, oxatriazolyl,thiadiazolyl, oxadiazolyl, morpholinyl, thiazolyl, thiazolidinyl,isothiazolyl, isothiazolidinyl, dithiazolyl, dithiazolidinyl,tetrahydrofuryl, and benzofused derivatives thereof. In certainembodiments, a “substituted heterocycle, or heterocycloalkyl orheterocyclic” group is utilized and as used herein, refers to aheterocycle, or heterocycloalkyl or heterocyclic group, as definedabove, substituted by the independent replacement of one, two or threeof the hydrogen atoms thereon with but are not limited to aliphatic;alicyclic; heteroaliphatic; heterocyclic; aromatic; heteroaromatic;aryl; heteroaryl; alkylaryl; heteroalkylaryl; alkylheteroaryl;heteroalkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy;alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH;—NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂;—CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x);—OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR % (CO)R_(x)wherein each occurrence of R_(x) independently includes, but is notlimited to, aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl,heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic,alicyclic, heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroarylsubstituents described above and herein may be substituted orunsubstituted, branched or unbranched, saturated or unsaturated, andwherein any of the aromatic, heteroaromatic, aryl or heteroarylsubstitutents described above and herein may be substituted orunsubstituted. Additional examples or generally applicable substituentsare illustrated by the specific embodiments shown in the Examples, whichare described herein.

Additionally, it will be appreciated that any of the alicyclic orheterocyclic moieties described above and herein may comprise an aryl orheteroaryl moiety fused thereto. Additional examples of generallyapplicable substituents are illustrated by the specific embodimentsshown in the Examples that are described herein. The terms “halo” and“halogen” as used herein refer to an atom selected from fluorine,chlorine, bromine and iodine.

The terms “halo” and “halogen” as used herein refer to an atom selectedfrom fluorine, chlorine, bromine and iodine.

The term “haloalkyl” denotes an alkyl group, as defined above, havingone, two, or three halogen atoms attached thereto and is exemplified bysuch groups as chloromethyl, bromoethyl, trifluoromethyl, and the like.

The term “amino”, as used herein, refers to a primary (—NH₂), secondary(—NH_(x)), tertiary (—NR_(x)R_(y)) or quaternary (—N⁺R_(x)R_(y)R_(x))amine, where R_(x), R_(y) and R_(z) are independently an aliphatic,alicyclic, heteroaliphatic, heterocyclic, aryl, or heteroaryl moiety, asdefined herein. Examples of amino groups include, but are not limitedto, methylamino, dimethylamino, ethylamino, diethylamino,diethylaminocarbonyl, methylethylamino, iso-propylamino, piperidino,trimethylamino, and propylamino.

The term “alkylidene”, as used herein, refers to a substituted orunsubstituted, linear or branched saturated divalent radical consistingsolely of carbon and hydrogen atoms, having from one to n carbon atoms,having a free valence “-” at both ends of the radical. In certainembodiments, the alkylidene moiety has 1 to 6 carbon atoms.

The term “alkenylidene”, as used herein, refers to a substituted orunsubstituted, linear or branched unsaturated divalent radicalconsisting solely of carbon and hydrogen atoms, having from two to ncarbon atoms, having a free valence “-” at both ends of the radical, andwherein the unsaturation is present only as double bonds and wherein adouble bond can exist between the first carbon of the chain and the restof the molecule. In certain embodiments, the alkenylidene moiety has 2to 6 carbon atoms.

The term “alkynylidene”, as used herein, refers to a substituted orunsubstituted, linear or branched unsaturated divalent radicalconsisting solely of carbon and hydrogen atoms, having from two to ncarbon atoms, having a free valence “-” at both ends of the radical, andwherein the unsaturation is present only as triple or double bonds andwherein a triple or double bond can exist between the first carbon ofthe chain and the rest of the molecule. In certain embodiments, thealkynylidene moiety has 2 to 6 carbon atoms.

Unless otherwise indicated, as used herein, the terms “alkyl”,“alkenyl”, “alkynyl”, “heteroalkyl”, “heteroalkenyl”, “heteroalkynyl”,“alkylidene”, “alkenylidene”, -(alkyl)aryl, -(heteroalkyl)aryl,-(heteroalkyl)aryl, -(heteroalkyl)heteroaryl, and the like encompasssubstituted and unsubstituted, and linear and branched groups.Similarly, the terms “aliphatic”, “heteroaliphatic”, and the likeencompass substituted and unsubstituted, saturated and unsaturated, andlinear and branched groups. Similarly, the terms “cycloalkyl”,“heterocycle”, “heterocyclic”, and the like encompass substituted andunsubstituted, and saturated and unsaturated groups. Additionally, theterms “cycloalkenyl”, “cycloalkynyl”, “heterocycloalkenyl”,“heterocycloalkynyl”, “aromatic”, “heteroaromatic, “aryl”, “heteroaryl”and the like encompass both substituted and unsubstituted groups.

The phrase, “pharmaceutically acceptable derivative”, as used herein,denotes any pharmaceutically acceptable salt, ester, or salt of suchester, of such compound, or any other adduct or derivative which, uponadministration to a patient, is capable of providing (directly orindirectly) a compound as otherwise described herein, or a metabolite orresidue thereof. Pharmaceutically acceptable derivatives thus includeamong others pro-drugs. A pro-drug is a derivative of a compound,usually with significantly reduced pharmacological activity, whichcontains an additional moiety, which is susceptible to removal in vivoyielding the parent molecule as the pharmacologically active species. Anexample of a pro-drug is an ester, which is cleaved in vivo to yield acompound of interest. Pro-drugs of a variety of compounds, and materialsand methods for derivatizing the parent compounds to create thepro-drugs, are known and may be adapted to the present invention.Pharmaceutically acceptable derivatives also include “reversepro-drugs.” Reverse pro-drugs, rather than being activated, areinactivated upon absorption. For example, as discussed herein, many ofthe ester-containing compounds of the invention are biologically activebut are inactivated upon exposure to certain physiological environmentssuch as a blood, lymph, serum, extracellular fluid, etc. which containesterase activity. The biological activity of reverse pro-drugs andpro-drugs may also be altered by appending a functionality onto thecompound, which may be catalyzed by an enzyme. Also, included areoxidation and reduction reactions, including enzyme-catalyzed oxidationand reduction reactions. Certain exemplary pharmaceutical compositionsand pharmaceutically acceptable derivatives will be discussed in moredetail herein below.

By the term “protecting group”, has used herein, it is meant that aparticular functional moiety, e.g., O, S, or N, is temporarily blockedso that a reaction can be carried out selectively at another reactivesite in a multifunctional compound. In preferred embodiments, aprotecting group reacts selectively in good yield to give a protectedsubstrate that is stable to the projected reactions; the protectinggroup must be selectively removed in good yield by readily available,preferably nontoxic reagents that do not attack the other functionalgroups; the protecting group forms an easily separable derivative (morepreferably without the generation of new stereogenic centers); and theprotecting group has a minimum of additional functionality to avoidfurther sites of reaction. As detailed herein, oxygen, sulfur, nitrogenand carbon protecting groups may be utilized. For example, in certainembodiments, as detailed herein, certain exemplary oxygen protectinggroups are utilized. These oxygen protecting groups include, but are notlimited to methyl ethers, substituted methyl ethers (e.g., MOM(methoxymethyl ether), MTM (methylthiomethyl ether), BOM(benzyloxymethyl ether), PMBM or MPM (p-methoxybenzyloxymethyl ether),to name a few), substituted ethyl ethers, substituted benzyl ethers,silyl ethers (e.g., TMS (trimethylsilyl ether), TES(triethylsilylether), TIPS (triisopropylsilyl ether), TBDMS(t-butyldimethylsilyl ether), tribenzyl silyl ether, TBDPS(t-butyldiphenyl silyl ether), to name a few), esters (e.g., formate,acetate, benzoate (Bz), trifluoroacetate, dichloroacetate, to name afew), carbonates, cyclic acetals and ketals. In certain other exemplaryembodiments, nitrogen protecting groups are utilized. These nitrogenprotecting groups include, but are not limited to, carbamates (includingmethyl, ethyl and substituted ethyl carbamates (e.g., Troc), to name afew) amides, cyclic imide derivatives, N-Alkyl and N-Aryl amines, iminederivatives, and enamine derivatives, to name a few. Certain otherexemplary protecting groups are detailed herein, however, it will beappreciated that the present invention is not intended to be limited tothese protecting groups; rather, a variety of additionalequivalent-protecting groups can be readily identified using the abovecriteria and utilized in the present invention. Additionally, a varietyof protecting groups are described in “Protective Groups in OrganicSynthesis” Third Ed. Greene, T. W. and Wuts, P. G., Eds., John Wiley &Sons, New York: 1999, the entire contents of which are herebyincorporated by reference.

The term “solid support”, as used herein, refers to a material having arigid or semi-rigid surface. Such materials will preferably take theform of small beads, pellets, disks, chips, dishes, multi-well plates,glass slides, wafers, or the like, although other forms may be used. Insome embodiments, at least one surface of the substrate will besubstantially flat. The term “surface” refers to any generallytwo-dimensional structure on a solid substrate and may have steps,ridges, kinks, terraces, and the like without ceasing to be a surface.

The term “polymeric support”, as used herein, refers to a soluble orinsoluble polymer to which an amino acid or other chemical moeity can becovalently bonded by reaction with a functional group of the polymericsupport. Many suitable polymeric supports are known, and include solublepolymers such as polyethylene glycols or polyvinyl alcohols, as well asinsoluble polymers such as polystyrene resins. A suitable polymericsupport includes functional groups such as those described below. Apolymeric support is termed “soluble” if a polymer, or apolymer-supported compound, is soluble under the conditions employed.However, in general, a soluble polymer can be rendered insoluble underdefined conditions. Accordingly, a polymeric support can be solubleunder certain conditions and insoluble under other conditions.

The term “linker,” as used herein, refers to a chemical moiety utilizedto attach a compound of interest to a solid support to facilitatesynthesis of inventive compounds or a linker may attach one portion of acompound to another portion of a compound. Preferably, the linkercomprises covalent bonds. Exemplary linkers are described herein. Itwill be appreciated that other linkers that are known in the art canalso be employed for the synthesis of the compounds of the invention.

“Compound”: The term “compound” or “chemical compound” as used hereincan include organometallic compounds, organic compounds, metals,transitional metal complexes, and small molecules. In certain preferredembodiments, polynucleotides are excluded from the definition ofcompounds. In other preferred embodiments, polynucleotides and peptidesare excluded from the definition of compounds. In a particularlypreferred embodiment, the term compounds refers to small molecules(e.g., preferably, non-peptidic and non-oligomeric) and excludespeptides, polynucleotides, transition metal complexes, metals, andorganometallic compounds.

“Small Molecule”: As used herein, the term “small molecule” refers to anon-peptidic, non-oligomeric organic compound either synthesized in thelaboratory or found in nature. Small molecules, as used herein, canrefer to compounds that are “natural product-like”, however, the term“small molecule” is not limited to “natural product-like” compounds.Rather, a small molecule is typically characterized in that it containsseveral carbon-carbon bonds, and has a molecular weight of less than1500, although this characterization is not intended to be limiting forthe purposes of the present invention. Examples of “small molecules”that occur in nature include, but are not limited to, taxol, dynemicin,and rapamycin. Examples of “small molecules” that are synthesized in thelaboratory include, but are not limited to, compounds described in Tanet al., (“Stereoselective Synthesis of over Two Million Compounds HavingStructural Features Both Reminiscent of Natural Products and Compatiblewith Miniaturized. Cell-Based Assays” J. Am. Chem. Soc. 120:8565, 1998;incorporated herein by reference). In certain other preferredembodiments, natural-product-like small molecules are utilized.

“Natural Product-Like Compound”: As used herein, the term “naturalproduct-like compound” refers to compounds that are similar to complexnatural products which nature has selected through evolution. Typically,these compounds contain one or more stereocenters, a high density anddiversity of functionality, and a diverse selection of atoms within onestructure. In this context, diversity of functionality can be defined asvarying the topology, charge, size, hydrophilicity, hydrophobicity, andreactivity to name a few, of the functional groups present in thecompounds. The term, “high density of functionality”, as used herein,can preferably be used to define any molecule that contains preferablythree or more latent or active diversifiable functional moieties. Thesestructural characteristics may additionally render the inventivecompounds functionally reminiscent of complex natural products, in thatthey may interact specifically with a particular biological receptor,and thus may also be functionally natural product-like.

“Metal chelator”: As used herein, the term “metal chelator” refers toany molecule or moiety that is capable of forming a complex (i.e.,“chelates”) with a metal ion. In certain exemplary embodiments, a metalchelator refers to any molecule or moiety that “binds” to a metal ion,in solution, making it unavailable for use in chemical/enzymaticreactions. In certain embodiments, the solution comprises aqueousenvironments under physiological conditions. Examples of metal ionsinclude, but are not limited to, Ca²⁺, Fe³⁺, Zn²⁺, Na⁺, etc. In certainembodiments, the metal chelator bind Zn²⁺, which is found at the activesite of HDACs. In certain embodiments, molecules of moieties thatprecipitate metal ions are not considered to be metal chelators.

As used herein the term “biological sample” includes, withoutlimitation, cell cultures or extracts thereof; biopsied materialobtained from an animal (e.g., mammal) or extracts thereof; and blood,saliva, urine, feces, semen, tears, or other body fluids or extractsthereof. For example, the term “biological sample” refers to any solidor fluid sample obtained from, excreted by or secreted by any livingorganism, including single-celled micro-organisms (such as bacteria andyeasts) and multicellular organisms (such as plants and animals, forinstance a vertebrate or a mammal, and in particular a healthy orapparently healthy human subject or a human patient affected by acondition or disease to be diagnosed or investigated). The biologicalsample can be in any form, including a solid material such as a tissue,cells, a cell pellet, a cell extract, cell homogenates, or cellfractions; or a biopsy, or a biological fluid. The biological fluid maybe obtained from any site (e.g. blood, saliva (or a mouth washcontaining buccal cells), tears, plasma, serum, urine, bile,cerebrospinal fluid, amniotic fluid, peritoneal fluid, and pleuralfluid, or cells therefrom, aqueous or vitreous humor, or any bodilysecretion), a transudate, an exudate (e.g. fluid obtained from anabscess or any other site of infection or inflammation), or fluidobtained from a joint (e.g. a normal joint or a joint affected bydisease such as rheumatoid arthritis, osteoarthritis, gout or septicarthritis). The biological sample can be obtained from any organ ortissue (including a biopsy or autopsy specimen) or may comprise cells(whether primary cells or cultured cells) or medium conditioned by anycell, tissue or organ. Biological samples may also include sections oftissues such as frozen sections taken for histological purposes.Biological samples also include mixtures of biological moleculesincluding proteins, lipids, carbohydrates and nucleic acids generated bypartial or complete fractionation of cell or tissue homogenates.Although the sample is preferably taken from a human subject, biologicalsamples may be from any animal, plant, bacteria, virus, yeast, etc. Theterm animal, as used herein, refers to humans as well as non-humananimals, at any stage of development, including, for example, mammals,birds, reptiles, amphibians, fish, worms and single cells. Cell culturesand live tissue samples are considered to be pluralities of animals. Incertain exemplary embodiments, the non-human animal is a mammal (e.g., arodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep,cattle, a primate, or a pig). An animal may be a transgenic animal or ahuman clone. If desired, the biological sample may be subjected topreliminary processing, including preliminary separation techniques.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows examples from the three classes of inventivecompounds—tubacin, isotubacin, and isoisotubacin.

FIG. 2 shows a general synthetic scheme for compounds of the“isotubacin” class.

FIG. 3 shows an exemplary synthesis of isotubacin.

FIG. 4 shows a general synthetic scheme for compounds of the“isoisotubacin” class.

FIG. 5 shows an exemplary synthesis of isoisotubacin.

FIG. 6 shows exemplary epoxide-opening reactions useful in preparingvarious analogs of the inventive compounds. The scheme illustrates theuse of various nucleophiles to open the epoxide group to create the diolfunctionality later capped to create the isotubacin and isoisotubacinstructures.

FIG. 7 graphically depicts protein degradation pathways and thescientific rationale for combining bortezomib (VELCADE®) with HDAC6inhibitors (e.g., isotubacin, isoisotubacin) in the treatment of proteindegradation disorders. There are two pathways which degrademisfolded/unfolded proteins which are ubiquitinated. The former is theproteasome pathway, and the latter is the aggresome pathway, whichrequires HDAC 6 activity. Therefore inhibition of both pathways byspecific inhibitors, bortezomib (VELCADE®), and isotubacin orisoisotubacin, induced accumulation of cytotoxic misfolded/unfoldedproteins.

FIG. 8 is a schematic of the high-throughput immunofluorescencequantitative assay for acetylated tubulin versus acetylated lysine (asan indicator of acetylated histones) with resulting images.

FIG. 9 shows the chemical structure for Isotubacin (NKI-93-1). The1,3-dioxane core in tubacin derivatives is rotated 120°counter-clockwise to yield isotubacin.

FIG. 10 shows the synergy between isotubacin (NKI-93-1) and bortezomib(VELCADE®) in myeloma cell lines (A) MM.1S, and (B) RPMI cells.

FIG. 11 demonstrates the specificity of isotubacin (NKI-93-1) fortubulin acetylation versus lysine acetylation.

FIG. 12 shows the TDAC inhibitory activity of the compounds—tubacin,NKI-82-1, NKI-81-1, isotubacin (NKI-93-1), NKI-94-1, NKI-59-1-,NKI-60-1, DHM-Tubacin, and MAZ-1428.

FIG. 13 is a chart showing the HDAC inhibition and TDAC inhibition ofthe compounds—tubacin, DHM-Tubacin, NKI-59-1, NKI-60-1, NKI-82-1,NKI-84-1, NKI-94-1 NKI-81-1, and isotubacin (NKI-93-1).

FIG. 14 shows the binding of various compounds including isotubacin(NKI-93-1) to HSA.

DETAILED DESCRIPTION OF THE INVENTION

As discussed above, there remains a need for the development of novelinhibitors of histone deacetylases, tubulin histone deacetylases, andthe aggresome. In particular, inhibitors that are more potent and/ormore specific for their particular target than known HDAC and TDACinhibitors. HDAC inhibitors specific for a certain class or member ofthe HDAC family would be particularly useful both in the treatment ofproliferative diseases and protein deposition disorders and in the studyof HDACs. Inhibitors that are specific for HDAC versus TDAC and viceversa are also useful in treating disease and probing biologicalpathways. The present invention provides novel compounds, methods forthe synthesis thereof, pharmaceutical compositions thereof, and methodsof using these compounds to treat cancer, proliferative diseases,protein degradation disorders, and protein deposition disorders.

Compounds of the Invention

As discussed above, the present invention provides compounds useful forthe treatment of various diseases. In certain embodiments, the compoundsof the present invention are useful as inhibitors of histone or tubulindeacetylases and thus are useful as anti-cancer agents, and thus may beuseful in the treatment of cancer, by effecting tumor cell death orinhibiting the growth of tumor cells. In certain exemplary embodiments,the inventive anticancer agents are useful in the treatment of cancersand other proliferative disorders, including, but not limited to breastcancer, cervical cancer, colon and rectal cancer, leukemia, lung cancer,melanoma, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer,pancreatic cancer, prostate cancer, and gastric cancer, to name a few.In certain embodiments, the inventive anticancer agents are activeagainst leukemia cells and melanoma cells, and thus are useful for thetreatment of leukemias (e.g., myeloid, lymphocytic, myelocytic andlymphoblastic leukemias) and malignant melanomas. In certainembodiments, the compounds are useful in the treatment of multiplemyeloma. Additionally, the inventive compounds may also be useful in thetreatment of protozoal infections. The inventive compounds are alsouseful in the treatment of diseases associated with aberrant proteincatabolism, for example, protein degradation disorders, disordersassociated with misfolded proteins, and protein deposition disorders. Incertain embodiments, the compound are useful in the treatment of theprotein deposition disorders, Wilson's disease, spinocerebellar ataxia,prion disease, Parkinson's disease, Huntington's disease, familianamyotrophic lateral sclerosis, amyloidosis, Alzheimer's disease,Alexander's diseases, alcoholic liver disease, cystic fibrosis, Pick'sdisease, and Lewy body dementia. In certain exemplary embodiments, thecompounds of the invention are useful for disorders associated withhistone deacetylation activity. In certain exemplary embodiments, thecompounds of the invention are useful for disorders associated withtubulin deacetylation activity. In other exemplary embodiments, thecompounds of the invention are useful for disorders associated withaggresome activity. In certain embodiments, the compounds, particularlycompounds with an ester moiety, are useful in treating skin disorders.Exemplary skin disorders that may be treated using certain of theinventive compounds include cutaneous T-cell lymphoma (CTCL), psoriasis,hair loss, dermatitis, etc.

Compounds of this invention comprise those, as set forth above anddescribed herein, and are illustrated in part by the various classes,subclasses, subgenera, and species disclosed herein. The inventionprovides compounds, e.g., compounds useful in the methods,pharmaceutical compositions, kits, and packaged compositions of theinvention. The inventive compounds are inhibitors of histonedeacetylases, tubulin deacetylases, or the aggresome. The compounds ofthe invention are typically based on a 1,3-dioxane core structure.

Exemplary classes of compounds of the invention include compounds of theformula:

wherein

R₁ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(A); —C(═O)R_(A);—CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂;—NHC(O)R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety;

R₂ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(B); —C(═O)R_(B);—CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂;—NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; and

R₃ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(C); —C(═O)R_(C);—CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N(R_(C))₂;—NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; andpharmaceutically acceptable salts and derivatives thereof. In certainembodiments, R₁ comprises a metal chelating functional group (e.g.,hydroxyamic acids, thiols, carboxylic acids, ortho-aminoanilides, etc.).

As will be appreciated by one of skill in this art, the 1,3-dioxane corehas been rotated 120° in each of the two classes of compounds ascompared to the 1,3-dioxane core of tubacin and its derivatives.

The invention also provides compounds of the isotubacin class. Thesecompounds are of the formula:

A general synthetic scheme for preparing compounds of this class isshown in FIG. 2. FIG. 3 is a synthetic scheme showing the synthesis ofisotubacin.

In certain embodiments, the compounds of this second class are one ofthe formulae below with the stereochemistry as shown:

In certain embodiments, R₁ is a substituted phenyl ring. In certainparticular embodiments, R₁ is of the formula:

wherein R₁′ is

wherein Y is NH or O; L is a linker moiety; and A comprises a functionalgroup that inhibits histone or tubulin deacetylase.

In certain embodiments, R₁ is of the formula:

In other embodiments, R₁ is of the formula:

In certain embodiments, Y is NH. In other embodiments, Y is O. Incertain embodiments, L is a substituted or unsubstituted, cyclic oracyclic, branched or unbranched aliphatic moiety; a substituted orunsubstituted, cyclic or acyclic, branched or unbranched heteroaliphaticmoiety; a substituted or unsubstituted aryl moiety; a substituted orunsubstituted heteroaryl moiety. In certain embodiments, L is asubstituted or unsubstituted, cyclic or acyclic, branched or unbranchedaliphatic moiety. In certain embodiments, L is C₁-C₂₀ alkylidene,preferably C₁ to C₁₂ alkylidene, more preferably C₄-C₇ alkylidene. Incertain embodiments, L is C₁-C₂₀ alkenylidene, preferably C₁ to C₁₂alkenylidene, more preferably C₄-C₇ alkenylidene. In certainembodiments, L is C₁-C₂₀ alkynylidene, preferably C₁ to C₁₂alkynylidene, more preferably C₄-C₇ alkynylidene. In certainembodiments, L is a substituted or unsubstituted, cyclic or acyclic,branched or unbranched heteroaliphatic moiety. In certain embodiments, Lcomprises a cyclic ring system, wherein the rings may be aryl,heteroaryl, non-aromatic carbocyclic, or non-aromatic heterocyclic. Instill other embodiments, L comprises a substituted or unsubstitutedheteroaryl moiety. In certain particular embodiments, L comprises aphenyl ring. In certain embodiments, L comprises multiple phenyl rings(e.g., one, two, three, or four phenyl rings).

In certain embodiments, L is

wherein n is an integer between 1 and 4, inclusive; preferably, between1 and 3, inclusive; more preferably, 1 or 2; and R₁ is is hydrogen;halogen; cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(A); —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A);—SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂; —NHR_(A); —NHC(O)R_(A); or—C(R_(A))₃; wherein each occurrence of R_(A) is independently ahydrogen, a protecting group, an aliphatic moiety, a heteroaliphaticmoiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino,heteroaryloxy; or heteroarylthio moiety. In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclic alkylchain. In certain embodiments, L is

In other embodiments, L is

In certain other embodiments, L is

In other embodiments, L is

In yet other embodiments, L is

In certain embodiments, L is a substituted, acyclic aliphatic chain. Incertain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclicheteroaliphatic chain. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive; and R′ is hydrogen, C₁-C₆aliphatic, heteroaliphatic, aryl, heteroaryl, or acyl. In certainparticular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain embodiments, Acomprises a metal chelating functional group. For example, A comprises aZn²⁺ chelating group. In certain embodiments, A comprises a functionalgroup selected group consisting of:

In certain embodiments, A comprises hydroxamic acid

or a salt thereof. In other embodiments, A comprises the formula:

In certain particular embodiments, A comprises the formula:

In other embodiments, A comprises a carboxylic, acid (—CO₂H). In otherembodiments, A comprises an o-aminoanilide

In other embodiments, A comprises an o-hydroxyanilide

In yet other embodiments, A comprises a thiol (—SH). In certainembodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

In other particular embodiments, R₁′ is

In certain embodiments, R₂ is hydrogen. In other embodiments, R₂ ishydroxyl or a protected hydroxyl group. In certain embodiments, R₂ isalkoxy. In yet other embodiments, R₂ is a lower alkyl, alkenyl, oralkynyl group. In certain embodiments, R₂ is —(CH₂)_(m)—X(R_(B))_(n),wherein X is O, S, N, or C, preferably O, S, or N; n is 1, 2, or 3; andm is an integer between 1 and 6, inclusive. In certain embodiments, R₂is —CH₂—X(R_(B))_(n), wherein X is O, S, N, or C, preferably O, S, or N;and n is 1, 2, or 3. In certain embodiments, R₂ is —CH₂—OR_(B). In otherembodiments, R₂ is —CH₂—SR_(B). In yet other embodiments, R₂ is—CH₂—R_(B). In other embodiments, R₂ is —CH₂—N(R_(B))₂. In still otherembodiments, R₂ is —CH₂—NHR_(B). In certain embodiments of theinvention, R_(B) is one of:

wherein m and p are each independently integers from 0 to 3; q₁ is aninteger from 1 to 6; R^(2C) is hydrogen, lower alkyl or a nitrogenprotecting group; and each occurrence of R^(2B) is independentlyhydrogen, halogen, —CN, or WR^(W1) wherein W is O, S, NR^(W2), —C(═O),—S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2), —NR^(W2)C(═O); whereineach occurrence of R^(W1) and R^(W2) is independently hydrogen, aprotecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl,heterocyclic, aryl or heteroaryl moiety, or, when W is NR^(W2), R^(W1)and R^(W2), taken together with the nitrogen atom to which they areattached, form a heterocyclic or heteroaryl moiety; or any two adjacentoccurrences of R^(2B), taken together with the atoms to which they areattached, form a substituted or unsubstituted, saturated or unsaturatedalicyclic or heterocyclic moiety, or a substituted or unsubstituted arylor heteroaryl moiety. In certain embodiments of the invention, R_(B) isone of the structures:

wherein m is an integer from 1 to 4; R^(2C) is hydrogen, lower alkyl ora nitrogen protecting group; and each occurrence of R^(2B) isindependently hydrogen, halogen, —CN, or WR^(W1) wherein W is O, S,NR^(W2), —C(═O—O), —S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2),—NR^(W2)C(═O); wherein each occurrence of R^(W1) and R^(W2) isindependently hydrogen, a protecting group, a prodrug moiety or analkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety,or, when W is NR^(W2), R^(W1) and R^(W2), taken together with thenitrogen atom to which they are attached, form a heterocyclic orheteroaryl moiety; or any two adjacent occurrences of R^(2B), takentogether with the atoms to which they are attached, form a substitutedor unsubstituted, saturated or unsaturated alicyclic or heterocyclicmoiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(R_(B))_(n) of —CH₂—X(R_(B))_(n) or—(CH₂)_(m)—X(R_(B))_(n) has one of the structures:

In certain embodiments, R₂ is

wherein X is N and Y is NH, S, or O. In other embodiments, R₂ is

In certain embodiments, R₂ is selected from one of the following:

In certain embodiments, R₃ is aliphatic. In other embodiments, R₃ isheteroaliphatic. In certain embodiments, R₃ is a substituted orunsubstituted aryl moiety. In certain embodiments, R₃ is a substitutedor unsubstituted heteroaromatic moiety. In certain embodiments, R₃ is amonocyclic moiety. In other embodiments, R₃ is a bicyclic moiety. In yetother embodiments, R₃ is a tricyclic moiety. In yet other embodiments,R₃ is a polycyclic moiety. In certain embodiments, R₃ is a substitutedor unsubstituted five- or six-membered aromatic or heteroaromaticmoiety. In certain embodiments, R₃ is a substituted or unsubstitutedsix-membered aromatic or heteroaromatic moiety. In certain embodiments,R₃ is a substituted or unsubstituted six-membered aromatic moiety. Incertain embodiments, R₃ is a substituted or unsubstituted six-memberedheteroaromatic moiety. In certain embodiments, R₃ is a substituted orunsubstituted non-aromatic carbocyclic or heterocyclic moiety. Incertain embodiments, R₃ is substituted or unsubstituted aryl. In certainembodiments, R₃ is substituted or unsubstituted phenyl. In certainembodiments, R₃ is

In certain particular embodiments, R₃ is monosubstituted phenyl. Incertain embodiments, R₃ is para-substituted phenyl. In certainembodiments, R₃ is

wherein R₃′ is hydrogen, a protecting group, a solid support unit, analkyl, acyl, cycloalkyl, heteroalkyl, heterocyclic, aryl, heteroaryl,-(alkyl)aryl, -(alkyl)heteroaryl, -(heteroalkyl)aryl, or-(heteroalkyl)heteroaryl moiety. In certain embodiments, R₃ is

In certain embodiments, R₃ is not

In other embodiments, R₃ is substituted or unsubstituted heteroaryl.

In certain embodiments, the invention provides compounds of the formula:

wherein R₁ and R₂ are defined as above;

n is an integer between 1 and 5, inclusive; and

each occurrence of R₃′ is independently hydrogen; halogen; cyclic oracyclic, substituted or unsubstituted, branched or unbranched aliphatic;cyclic or acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety.

In certain embodiments, n is 0, and the phenyl ring is unsubstituted.

In other embodiments, n is 1, and the compounds are one of the formulae:

In certain embodiments, the para-substitution pattern is preferred. Inother embodiments, the meta-substitution pattern is preferred. And inyet other embodiments, the ortho-substitution pattern is preferred.

In other embodiments, n is 2. Compounds of the invention includecompounds of one of the formulae:

In other embodiments, n is 3. In still other embodiments, n is 4, and inother embodiments, n is 5.

In certain embodiments, R₃′ is halogen, hydroxyl, protected hydroxyl,alkoxy, amino, alkylamino, dialkylamino, —NO₂, C₁-C₆ alkyl, C₁-C₆alkenyl, C₁-C₆ alkynyl, or acyl. In certain embodiments, R₃′ is —NO₂. Incertain embodiments, R₃′ is —CH₂OH. In certain embodiments, R₃′ is —NH₂.In certain embodiments, R₃′ is —H. In other embodiments, R₃′ is —OH. Inother embodiments, R₃′ is —CN. In yet other embodiments, R₃′ is —SCN. Instill other embodiments, R₃′ is acyl. In certain embodiments, R₃′ isacetyl. In other embodiments, R₃′ is —F. In other embodiments, R₃′ isCl. In other embodiments, R₃′ is —Br. In other embodiments, R₃′ is —I.In other embodiments, R₃′ is methyl, ethyl, n-propyl, iso-propyl,n-butyl, tert-butyl, or iso-butyl. In certain embodiments, R₃′ is vinyl.In certain embodiments, R₃′ is halogen-substituted alkyl (e.g.,trifluoromethyl). In certain embodiments, R₃′ is methoxy, ethyoxy,propoxy, butoxy, or pentoxy.

Exemplary compounds of this second “isotubacin” class include compoundsof the formula:

The invention also provides compounds of the isoisotubacin class. Thesecompounds are of the formula:

A general synthetic scheme for preparing compounds of this class isshown in FIG. 4. FIG. 5 is a synthetic scheme showing the synthesis ofisoisotubacin.

In certain embodiments, the compounds of this second class are one ofthe formulae below with the stereochemistry as shown:

In certain embodiments, R₁ is a substituted phenyl ring. In certainparticular embodiments, R₁ is of the formula:

wherein R₁′ is

wherein Y is NH or O; L is a linker moiety; and A comprises a functionalgroup that inhibits histone deacetylase.

In certain embodiments, R₁ is of the formula:

In other embodiments, R₁ is of the formula:

In certain embodiments, Y is NH. In other embodiments, Y is O. Incertain embodiments, L is a substituted or unsubstituted, cyclic oracyclic, branched or unbranched aliphatic moiety; a substituted orunsubstituted, cyclic or acyclic, branched or unbranched heteroaliphaticmoiety; a substituted or unsubstituted aryl moiety; a substituted orunsubstituted heteroaryl moiety. In certain embodiments, L is asubstituted or unsubstituted, cyclic or acyclic, branched or unbranchedaliphatic moiety. In certain embodiments, L is C₁-C₂₀ alkylidene,preferably C₁ to C₁₂ alkylidene, more preferably C₄-C₇ alkylidene. Incertain embodiments, L is C₁-C₂₀ alkenylidene, preferably C₁ to C₁₂alkenylidene, more preferably C₄-C₇ alkenylidene. In certainembodiments, L is C₁-C₂₀ alkynylidene, preferably C₁ to C₁₂alkynylidene, more preferably C₄-C₇ alkynylidene. In certainembodiments, L is a substituted or unsubstituted, cyclic or acyclic,branched or unbranched heteroaliphatic moiety. In certain embodiments, Lcomprises a cyclic ring system, wherein the rings may be aryl,heteroaryl, non-aromatic carbocyclic, or non-aromatic heterocyclic. Instill other embodiments, L comprises a substituted or unsubstitutedheteroaryl moiety. In certain particular embodiments, L comprises aphenyl ring. In certain embodiments, L comprises multiple phenyl rings(e.g., one, two, three, or four phenyl rings).

In certain embodiments, L is

wherein n is an integer between 1 and 4, inclusive; preferably, between1 and 3, inclusive; more preferably, 1 or 2; and R₁ is is hydrogen;halogen; cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(A); —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A);—SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂; —NR_(A); —NHC(O)R_(A); or—C(R_(A))₃; wherein each occurrence of R_(A) is independently ahydrogen, a protecting group, an aliphatic moiety, a heteroaliphaticmoiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino,heteroaryloxy; or heteroarylthio moiety. In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclic alkylchain. In certain embodiments, L is

In other embodiments, L is

In certain other embodiments, L is

In other embodiments, L is

In yet other embodiments, L is

In certain embodiments, L is a substituted, acyclic aliphatic chain. Incertain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclicheteroaliphatic chain. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive; and R′ is hydrogen, C₁-C₆aliphatic, heteroaliphatic, aryl, heteroaryl, or acyl. In certainparticular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and in is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain embodiments, Acomprises a metal chelating functional group. For example, A comprises aZn²⁺ chelating group. In certain embodiments, A comprises a functionalgroup selected group consisting of:

In certain embodiments, A comprises hydroxamic acid

or a salt thereof. In other embodiments, A comprises the formula:

In certain particular embodiments, A comprises the formula:

In other embodiments, A comprises a carboxylic acid (—CO₂H). In otherembodiments, A comprises an o-aminoanilide

In other embodiments, A comprises an o-hydroxyanilide

In yet other embodiments, A comprises a thiol (—SH). In certainembodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

In other particular embodiments, R₁′ is

In certain embodiments, R₂ is hydrogen. In other embodiments, R₂ ishydroxyl or a protected hydroxyl group. In certain embodiments, R₂ isalkoxy. In yet other embodiments, R₂ is a lower alkyl, alkenyl, oralkynyl group. In certain embodiments, R₂ is —CH₂—X(R_(B))_(n), whereinX is O, S, N, or C, preferably O, S, or N; and n is 1, 2, or 3. Incertain embodiments, R₂ is —CH₂—OR_(B). In other embodiments, R₂ is—CH₂—SR_(B). In yet other embodiments, R₂ is CH₂—R_(B). In otherembodiments, R₂ is —CH₂—N(R_(B))₂. In still other embodiments, R₂ is—CH₂—NHR_(B). In certain embodiments of the invention, R_(B) is one of:

wherein m and p are each independently integers from 0 to 3; q₁ is aninteger from 1 to 6; R^(2C) is hydrogen, lower alkyl or a nitrogenprotecting group; and each occurrence of R^(2B) is independentlyhydrogen, halogen, —CN, or WR^(W1) wherein W is O, S, NR^(W2), —C(═O),—S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2), —NR^(W2)C(═O); whereineach occurrence of R^(W1) and R^(W2) is independently hydrogen, aprotecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl,heterocyclic, aryl or heteroaryl moiety, or, when W is NR^(W2), R^(W1)and R^(W2), taken together with the nitrogen atom to which they areattached, form a heterocyclic or heteroaryl moiety; or any two adjacentoccurrences of R^(2B), taken together with the atoms to which they areattached, form a substituted or unsubstituted, saturated or unsaturatedalicyclic or heterocyclic moiety, or a substituted or unsubstituted arylor heteroaryl moiety. In certain embodiments of the invention, R_(B) isone of the structures:

wherein m is an integer from 1 to 4; R^(2C) is hydrogen, lower alkyl ora nitrogen protecting group; and each occurrence of R^(2B) isindependently hydrogen, halogen, —CN, or WR^(W1) wherein W is O, S,NR^(W2), —C(═O), —S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2),—NR^(W2)C(═O); wherein each occurrence of R^(W1) and R^(W2) isindependently hydrogen, a protecting group, a prodrug moiety or analkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety,or, when W is NR^(W2), R^(W1) and R^(W2), taken together with thenitrogen atom to which they are attached, form a heterocyclic orheteroaryl moiety; or any two adjacent occurrences of R^(2B), takentogether with the atoms to which they are attached, form a substitutedor unsubstituted, saturated or unsaturated alicyclic or heterocyclicmoiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(R_(B))_(n) has one of the structures:

In certain embodiments, R₂ is

wherein X is N and Y is NH, S, or O. In other embodiments, R₂ is

In certain embodiments, R₂ is selected from one of the following:

In certain embodiments, R₂ is a substituted or unsubstituted aryl orheteroaryl moiety. In certain embodiments, R₂ is a substituted orunsubstituted carbocyclic or heterocyclic moiety. The ring system of R₂may be monocyclic, bicyclic, tricyclic, or polycyclic. The rings makingup the ring system may be three-membered (e.g., oxiranyl, cyclopropyl,aziridinyl); four-membered; five-membered; six-membered; seven-membered;eight-membered; or n-membered. In bicyclic, tricyclic, or polycyclicring systems, the rings may be fused, spiro-linked, or linked via acovalent bond. In certain embodiments, R₂ is a substituted orunsubstituted, monocyclic aryl moiety. In certain embodiments, R₂ is asubstituted or unsubstituted, monocyclic phenyl moiety. In certainembodiments, R₂ is a substituted, monocyclic phenyl moiety. In certainembodiments, R₂ is unsubstituted phenyl. In certain embodiments, R₂ is amonosubstituted phenyl moiety. In other embodiments, R₂ is adisubstituted phenyl moiety. In yet other embodiments, R₂ is atrisubstituted phenyl moiety. In other embodiments, R₂ is a substitutedor unsubstituted, monocyclic heteroaryl moiety. In certain embodiments,R₂ is a substituted or unsubstituted pyridinyl moiety. In certainembodiments, R₂ is a substituted or unsubstituted pyrrolyl moiety. Incertain embodiments, R₂ is a substituted or unsubstituted imidazolylmoiety. In certain embodiments, R₂ is a substituted or unsubstitutedthiazolyl moiety. In certain embodiments, R₂ is a substituted orunsubstituted oxazolyl moiety. In certain embodiments, R₂ is asubstituted or unsubstituted furanyl moiety. In certain embodiments, R₂is a substituted or unsubstituted thiophenyl moiety. In certainembodiments, R₂ is a substituted or unsubstituted, monocycliccarbocyclic moiety. In certain embodiments, R₂ is a substituted orunsubstituted, cyclopentyl moiety. In certain embodiments, R₂ is asubstituted or unsubstituted, cyclohexyl moiety. In certain embodiments,R₂ is a substituted or unsubstituted, monocyclic heterocyclic moiety. Incertain embodiments, R₂ is a substituted or unsubstituted, piperidinylmoiety. In certain embodiments, R₂ is a substituted or unsubstituted,pyrrolidinyl moiety.

In certain embodiments, R₃ is a substituted or unsubstituted arylmoiety. In certain embodiments, R₃ is a substituted or unsubstitutedheteroaromatic moiety. In certain embodiments, R₃ is a monocyclicmoiety. In other embodiments, R₃ is a bicyclic moiety. In yet otherembodiments, R₃ is a tricyclic moiety. In yet other embodiments, R₃ is apolycyclic moiety. In certain embodiments, R₃ is a substituted orunsubstituted five- or six-membered aromatic or heteroaromatic moiety.In certain embodiments, R₃ is a substituted or unsubstitutedsix-membered aromatic or heteroaromatic moiety. In certain embodiments,R₃ is a substituted or unsubstituted six-membered aromatic moiety. Incertain embodiments, R₃ is a substituted or unsubstituted six-memberedheteroaromatic moiety. In certain embodiments, R₃ is a substituted orunsubstituted non-aromatic carbocyclic or heterocyclic moiety. Incertain embodiments, R₃ is unsubstituted aryl. In certain embodiments,R₃ is substituted aryl. In certain embodiments, R₃ is substituted orunsubstituted phenyl. In certain particular embodiments, R₃ ismonosubstituted phenyl. In certain embodiments, R₃ is

In certain embodiments, R₃ is para-substituted phenyl. In certainembodiments, R₃ is

wherein R₃′ is hydrogen, a protecting group, a solid support unit, analkyl, acyl, cycloalkyl, heteroalkyl, heterocyclic, aryl, heteroaryl,-(alkyl)aryl, -(alkyl)heteroaryl, -(heteroalkyl)aryl, or-(heteroalkyl)heteroaryl moiety. In certain embodiments, R₃ is

In certain embodiments, R₃ is not

In other embodiments, R₃ is substituted or unsubstituted heteroaryl.

In certain embodiments, the invention provides compounds of the formula:

wherein R₁ and R₂ are defined as above;

n is an integer between 1 and 5, inclusive; and

each occurrence of R₃′ is independently hydrogen; halogen; cyclic oracyclic, substituted or unsubstituted, branched or unbranched aliphatic;cyclic or acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety.

In certain embodiments, n is 0, and the phenyl ring is unsubstituted.

In other embodiments, n is 1, and the compounds are one of the formulae:

In certain embodiments, the para-substitution pattern is preferred. Inother embodiments, the meta-substitution pattern is preferred. And inyet other embodiments, the ortho-substitution pattern is preferred.

In other embodiments, n is 2. Compounds of the invention includecompounds of one of the formulae:

In other embodiments, n is 3. In still other embodiments, n is 4, and inother embodiments, n is 5.

In certain embodiments, R₃′ is halogen, hydroxyl, protected hydroxyl,alkoxy, amino, alkylamino, dialkylamino, —NO₂, C₁-C₆ alkyl, C₁-C₆alkenyl, C₁-C₆ alkynyl, or acyl. In certain embodiments, R₃′ is —NO₂. Incertain embodiments, R₃′ is —CH₂OH. In certain embodiments, R₃′ is —NH₂.In certain embodiments, R₃′ is —H. In other embodiments, R₃′ is —OH. Inother embodiments, R₃′ is —CN. In yet other embodiments, R₃′ is —SCN. Instill other embodiments, R₃′ is acyl. In certain embodiments, R₃′ isacetyl. In other embodiments, R₃′ is —F. In other embodiments, R₃′ is—I. In other embodiments, R₃′ is —Br. In other embodiments, R₃′ is —I.In other embodiments, R₃′ is methyl, ethyl, n-propyl, iso-propyl,n-butyl, tert-butyl, or iso-butyl. In certain embodiments, R₃′ is vinyl.In certain embodiments, R₃′ is halogen-substituted alkyl (e.g.,trifluoromethyl). In certain embodiments, R₃′ is methoxy, ethyoxy,propoxy, butoxy, or pentoxy.

Exemplary compounds of the “isoisotubacin” class include compounds ofthe formula:

In another embodiments, the invention provides dimers, trimers, ormultimers of HDAC inhibitors described herein. In certain embodiments,dimers are of the general formula,

wherein

each occurrence of R₁ comprises a functional group that inhibits histonedeacetylase or tubulin deacetylase, wherein the two R₁ groups may be thesame or different. Dimeric, trimeric, and multimeric HDAC inhibitors arefurther described in U.S. provisional patent application, U.S. Ser. No.60/773,510, filed Feb. 14, 2006, which is incorporated herein byreference. The tubacin structures in the dimeric compounds therein maybe changed to isotubacin and isoisotubacin structures. The dioxane coremay also provide for a trimer wherein R₂ is —R₁.

In certain embodiments, R₁ is a substituted phenyl ring. In certainparticular embodiments, R₁ is of the formula:

wherein R₁′ is

wherein Y is NH or O; L is a linker moiety; and A comprises a functionalgroup that inhibits histone or tubulin deacetylase.

In certain embodiments, R₁ is of the formula:

In other embodiments, R₁ is of the formula:

In certain embodiments, Y is NH. In other embodiments, Y is O. Incertain embodiments, L is a substituted or unsubstituted, cyclic oracyclic, branched or unbranched aliphatic moiety; a substituted orunsubstituted, cyclic or acyclic, branched or unbranched heteroaliphaticmoiety; a substituted or unsubstituted aryl moiety; a substituted orunsubstituted heteroaryl moiety. In certain embodiments, L is asubstituted or unsubstituted, cyclic or acyclic, branched or unbranchedaliphatic moiety. In certain embodiments, L is C₁-C₂₀ alkylidene,preferably C₁ to C₁₂ alkylidene, more preferably C₄-C₇ alkylidene. Incertain embodiments, L is C₁-C₂₀ alkenylidene, preferably C₁ to C₁₂alkenylidene, more preferably C₄-C₇ alkenylidene. In certainembodiments, L is C₁-C₂₀ alkynylidene, preferably C₁ to C₁₂alkynylidene, more preferably C₄-C₇ alkynylidene. In certainembodiments, L is a substituted or unsubstituted, cyclic or acyclic,branched or unbranched heteroaliphatic moiety. In certain embodiments, Lcomprises a cyclic ring system, wherein the rings may be aryl,heteroaryl, non-aromatic carbocyclic, or non-aromatic heterocyclic. Instill other embodiments, L comprises a substituted or unsubstitutedheteroaryl moiety. In certain particular embodiments, L comprises aphenyl ring. In certain embodiments, L comprises multiple phenyl rings(e.g., one, two, three, or four phenyl rings).

In certain embodiments, L is

wherein n is an integer between 1 and 4, inclusive; preferably, between1 and 3, inclusive; more preferably, 1 or 2; and R₁ is is hydrogen;halogen; cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(A); —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A);—SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂; —NHR_(A); —NHC(O)R_(A); or—C(R_(A))₃; wherein each occurrence of R_(A) is independently ahydrogen, a protecting group, an aliphatic moiety, a heteroaliphaticmoiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino,heteroaryloxy; or heteroarylthio moiety. In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclic alkylchain. In certain embodiments, L is

In other embodiments, L is

In certain other embodiments, L is

In other embodiments, L is

In yet other embodiments, L is

In certain embodiments, L is a substituted, acyclic aliphatic chain. Incertain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclicheteroaliphatic chain. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain particularembodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive; and R′ is hydrogen, C₁-C₆aliphatic, heteroaliphatic, aryl, heteroaryl, or acyl. In certainparticular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between0 and 5, inclusive; and m is an integer between 0 and 10, inclusive;preferably, between 0 and 5, inclusive. In certain embodiments, Acomprises a metal chelating functional group. For example, A comprises aZn²⁺ chelating group. In certain embodiments, A comprises a functionalgroup selected group consisting of:

In certain embodiments, A comprises hydroxamic acid

or a salt thereof. In other embodiments, A comprises the formula:

In certain particular embodiments, A comprises the formula:

In other embodiments, A comprises a carboxylic acid (—CO₂H), In otherembodiments, A comprises an o-aminoanilide

In other embodiments, A comprises an o-hydroxyanilide

In yet other embodiments, A comprises a thiol (—SH). In certainembodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

wherein n is an integer between 0 and 15, inclusive; preferably, between0 and 10, inclusive; more preferably, between 1 and 8, inclusive; evenmore preferably, 4, 5, 6, 7, or 8. In certain embodiments, R₁′ is

In other particular embodiments, R₁′ is

In certain embodiments of the invention, inventive compounds based onthe structure of isotubacin are of the formula:

wherein

each occurrence of R₁′ is defined as above and both occurrences of R₁′are the same or different; and

R₂ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(B); —C(═O)R_(B);—CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂;—NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety. In certainembodiments, R₂ is hydrogen. In other embodiments, R₂ is hydroxyl or aprotected hydroxyl group. In certain embodiments, R₂ is alkoxy. In yetother embodiments, R₂ is a lower alkyl, alkenyl, or alkynyl group. Incertain embodiments, R₂ is —CH₂—X(R_(B))_(n), wherein X is O, S, N, orC, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments,R₂ is —CH₂—OR_(B). In other embodiments, R₂ is —CH₂—SR_(B). In yet otherembodiments, R₂ is —CH₂—R_(B). In other embodiments, R₂ is—CH₂—N(R_(B))₂. In still other embodiments, R₂ is —CH₂—NHR_(B). Incertain embodiments of the invention, R_(B) is one of:

wherein m and p are each independently integers from 0 to 3; q₁ is aninteger from 1 to 6; R^(2C) is hydrogen, lower alkyl or a nitrogenprotecting group; and each occurrence of R^(2B) is independentlyhydrogen, halogen, —CN, or WR^(W1) wherein W is O, S, NR^(W2), —C(═O),—S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2), —NR^(W2)C(═O); whereineach occurrence of R^(W1) and R^(W2) is independently hydrogen, aprotecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl,heterocyclic, aryl or heteroaryl moiety, or, when W is NR^(W2), R^(W1)and R^(W2), taken together with the nitrogen atom to which hey areattached, form a heterocyclic or heteroaryl moiety; or any two adjacentoccurrences of R^(2B), taken together with the atoms to which they areattached, form a substituted or unsubstituted, saturated or unsaturatedalicyclic or heterocyclic moiety, or a substituted or unsubstituted arylor heteroaryl moiety. In certain embodiments of the invention, R_(B) isone of the structures:

wherein m is an integer from 1 to 4; R^(2C) is hydrogen, lower alkyl ora nitrogen protecting group; and each occurrence of R^(2B) isindependently hydrogen, halogen, —CN, or WR^(W1) wherein W is O, S,NR^(W2), —C(═O), —S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2),—NR^(W2)C(═O); wherein each occurrence of R^(W1) and R^(W2) isindependently hydrogen, a protecting group, a prodrug moiety or analkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety,or, when W is NR^(W2), R^(W1) and R^(W2), taken together with thenitrogen atom to which they are attached, form a heterocyclic orheteroaryl moiety; or any two adjacent occurrences of R^(2B), takentogether with the atoms to which they are attached, form a substitutedor unsubstituted, saturated or unsaturated alicyclic or heterocyclicmoiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(R_(B))_(n) of —CH₂—X(R_(B))_(n) has one ofthe structures:

In certain embodiments, R₂ is

wherein X is N and Y is NH, S, or O. In other embodiments, R₂ is

In certain embodiments of the invention, the stereochemistry of formulais chosen from one of the following:

In certain embodiments of the invention, compounds are of the formula:

wherein

A, B, and R₂ are defined as above;

X is O or NH;

n is an integer between 1 and 20, inclusive; preferably, between 1 and12, inclusive; more preferably between 2 and 8, inclusive. In certainembodiments, n is 2, 3, 4, 5, 6, 7, or 8; preferably, 6. In certainembodiments, X is NH. In other embodiments, X is O.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above;

n is an integer between 1 and 20, inclusive; preferably, between 1 and12, inclusive; more preferably between 2 and 8, inclusive. In certainembodiments, n is 2, 3, 4, 5, 6, 7, or 8; preferably, 6.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above.

In certain embodiments of the invention, compounds are of the formula:

In certain embodiments of the invention, inventive compounds based onthe structure of isoisotubacin are of the formula:

wherein

each occurrence of R₁′ is independently as defined above and bothoccurrences of R₁′ are the same or different; and

R₂ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(B); —C(═O)R_(B);—CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂;—NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety. In certainembodiments, R₂ is hydrogen. In other embodiments, R₂ is hydroxyl or aprotected hydroxyl group. In certain embodiments, R₂ is alkoxy. In yetother embodiments, R₂ is a lower alkyl, alkenyl, or alkynyl group. Incertain embodiments, R₂ is —CH₂—X(R_(B))_(n), wherein X is O, S, N, orC, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments,R₂ is —CH₂—OR_(B). In other embodiments, R₂ is —CH₂—SR_(B). In yet otherembodiments, R₂ is —CH₂—R_(B). In other embodiments, R₂ is—CH₂—N(R_(B))₂. In still other embodiments, R₂ is —CH₂—NHR_(B). Incertain embodiments of the invention, R_(B) is one of:

wherein m and p are each independently integers from 0 to 3; q₁ is aninteger from 1 to 6; R^(2C) is hydrogen, lower alkyl or a nitrogenprotecting group; and each occurrence of R^(2B) is independentlyhydrogen, halogen, —CN, or WR^(W1) wherein W is O, S, NR^(W2), —C(═O),—S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2), NR^(W2)C(═O); whereineach occurrence of R^(W1) and R^(W2) is independently hydrogen, aprotecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl,heterocyclic, aryl or heteroaryl moiety, or, when W is NR^(W2), R^(W1)and R^(W2), taken together with the nitrogen atom to which they areattached, form a heterocyclic or heteroaryl moiety; or any two adjacentoccurrences of R^(2B), taken together with the atoms to which they areattached, form a substituted or unsubstituted, saturated or unsaturatedalicyclic or heterocyclic moiety, or a substituted or unsubstituted arylor heteroaryl moiety. In certain embodiments of the invention, R_(B) isone of the structures:

wherein m is an integer from 1 to 4; R^(2C) is hydrogen, lower alkyl ora nitrogen protecting group; and each occurrence of R_(2B) isindependently hydrogen, halogen, —CN, or WR^(W1) wherein W is O, S,NR^(W2), —C(═O), —S(═O), —SO₂, —C(═O)O—, —OC(═O), —C(═O)NR^(W2),NR^(W2)C(═O); wherein each occurrence of R^(W1) and R^(W2) isindependently hydrogen, a protecting group, a prodrug moiety or analkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety,or, when W is NR^(W2), R^(W1) and R^(W2), taken together with thenitrogen atom to which they are attached, form a heterocyclic orheteroaryl moiety; or any two adjacent occurrences of R^(2B), takentogether with the atoms to which they are attached, form a substitutedor unsubstituted, saturated or unsaturated alicyclic or heterocyclicmoiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(R_(B))_(n) of —CH₂—X(R_(B))_(n) has one ofthe structures:

In certain embodiments, R₂ is

wherein X is N and Y is NH, S, or O. In other embodiments, R₂ is

In certain embodiments of the invention, the stereochemistry of formulais chosen from one of the following:

In certain embodiments of the invention, compounds are of the formula:

wherein

A, B, and R₂ are defined as above;

X is O or NH;

n is an integer between 1 and 20, inclusive; preferably, between 1 and12, inclusive; more preferably between 2 and 8, inclusive. In certainembodiments, n is 2, 3, 4, 5, 6, 7, or 8; preferably, 6. In certainembodiments, X is NH. In other embodiments, X is O.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above;

n is an integer between 1 and 20, inclusive; preferably, between 1 and12, inclusive; more preferably between 2 and 8, inclusive. In certainembodiments, n is 2, 3, 4, 5, 6, 7, or 8; preferably, 6.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above.

In certain embodiments of the invention, compounds are of the formula:

wherein

R₂ is defined as above.

In certain embodiments of the invention, compounds are of the formula:

Some of the foregoing compounds can comprise one or more asymmetriccenters, and thus can exist in various isomeric forms, e.g.,stereoisomers and/or diastereomers. Thus, inventive compounds andpharmaceutical compositions thereof may be in the form of an individualenantiomer, diastereomer or geometric isomer, or may be in the form of amixture of stereoisomers. In certain embodiments, the compounds of theinvention are enantiopure compounds. In certain other embodiments,mixtures of stereoisomers or diastereomers are provided.

Furthermore, certain compounds, as described herein may have one or moredouble bonds that can exist as either the Z or E isomer, unlessotherwise indicated. The invention additionally encompasses thecompounds as individual isomers substantially free of other isomers andalternatively, as mixtures of various isomers, e.g., racemic mixtures ofstereoisomers. In addition to the above-mentioned compounds per se, thisinvention also encompasses pharmaceutically acceptable derivatives ofthese compounds and compositions comprising one or more compounds of theinvention and one or more pharmaceutically acceptable excipients oradditives.

Compounds of the invention may be prepared by crystallization ofcompound of any of the formula above under different conditions and mayexist as one or a combination of polymorphs of compound of any generalformula above forming part of this invention. For example, differentpolymorphs may be identified and/or prepared using different solvents,or different mixtures of solvents for recrystallization; by performingcrystallizations at different temperatures; or by using various modes ofcooling, ranging from very fast to very slow cooling duringcrystallizations. Polymorphs may also be obtained by heating or meltingthe compound followed by gradual or fast cooling. The presence ofpolymorphs may be determined by solid probe NMR spectroscopy, IRspectroscopy, differential scanning calorimetry, powder X-raydiffractogram and/or other techniques. Thus, the present inventionencompasses inventive compounds, their derivatives, their tautomericforms, their stereoisomers, their polymorphs, their pharmaceuticallyacceptable salts their pharmaceutically acceptable solvates andpharmaceutically acceptable compositions containing them.

Synthetic Overview

As described above, the present invention provides novel compounds,specifically compounds having a 1,3-dioxane core as described above. Thesynthesis of compounds of the “tubacin” class has been described inpreviously filed U.S. patent applications, U.S. Ser. No. 11/386,959,filed Mar. 22, 2006; U.S. Ser. No. 60/664,470, filed Mar. 22, 2005; U.S.Ser. No. 60/289,850, filed May 9, 2001; U.S. Ser. No. 10/144,316, filedMay 9, 2002; and U.S. Ser. No. 10/621,276, filed Jul. 17, 2003; each ofwhich is incorporated herein by reference. As would be appreciated byone of skill in this art, the various reactions and synthetic schemesdescribed in these patent applications may be used in preparing theinventive compounds described herein.

A general synthetic scheme for preparing compounds of the isotubacinclass is shown in FIG. 2. A particular exemplary synthesis of isotubacinis shown in FIG. 3. It will be appreciated that for compounds of theformula

a method for the synthesis of the core structure is provided comprisingsteps of:

providing an epoxy alcohol having the structure:

reacting the epoxy alcohol with a reagent having the structure R_(B)XHunder suitable conditions to generate a diol having the core structure:

reducing the nitro group to generate a diol having the core structure:

reacting the amino group with acylating agent to generate a diol havingthe core structure:

reacting the diol with a reagent having the structure R₃CH(OMe)₂ orother acetal under suitable conditions to generate a scaffold having thecore structure:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone deacetylase as described herein;

R_(B) is hydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety;

X is —O—, —C(R′)₂—, —S—, or —NR′—, wherein R′ is hydrogen, a protectinggroup, or an aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic or heteroaromatic moiety; and

R³ is an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic,or heteroaromatic moiety. In certain embodiments rather than reactingthe diol with a reagent having the structure R₃CH(OMe)₂ or other acetal,the diol is reacted with an aldehyde of structure R₃CHO. In otherembodiments, the methods optionally comprises additional steps ofprotecting and/or deprotecting functional groups of R_(B), R₁, R₁′, R₂,or R₃. In other embodiments, the method optionally comprises additionalsteps of modifying functional groups of R_(B), R₁, R₁′, R₂, or R₃. Forexample, in FIG. 2 the methyl ester functionality of R₁′ is converted toa hydroxamic acid functional group.

In certain exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain other exemplary embodiments, the epoxy alcohol has thestructure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain other exemplary embodiments, the epoxy alcohol has thestructure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain exemplary embodiments, A is a hydroxamic acid. In certainembodiments, L is an C₁-C₈ alkylidene moiety. In certain embodiments, R₃is a substituted or unsubstituted phenyl. In certain particularembodiments, R₃ is an unsubstituted phenyl. In certain embodiments, R₃is a substituted phenyl. In certain embodiments, X is O. In otherembodiments, X is S. In certain embodiments, X is NH or NR_(B). Incertain embodiments, R_(B) is substituted or unsubstituted aryl orheteroaryl.

A general synthetic scheme for preparing compounds of the“isoisotubacin” class is shown in FIG. 6. A particular exemplarysynthesis of isotubacin is shown in FIG. 7. It will be appreciated thatfor compounds of the formula

a method for the synthesis of the core structure is provided comprisingsteps of:

providing an beta-hydroxy ketone having the structure:

reducing the ketone to generate a diol having the core structure:

reducing the nitro group to generate a diol having the core structure:

reacting the amino group with acylating agent to generate a diol havingthe core structure:

reacting the diol with a reagent having the structure R₂CH(OMe)₂ orother acetal under suitable conditions to generate a scaffold having thecore structure:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone or tubulin deacetylase asdescribed herein;

R_(B) is hydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety;

X is —, —C(R′)₂—, —S—, or —NR′—, wherein R′ is hydrogen, a protectinggroup, or an aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic or heteroaromatic moiety; and

R³ is an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic,or heteroaromatic moiety. In certain embodiments rather than reactingthe diol with a reagent having the structure R₂CH(OMe)₂ or other acetal,the diol is reacted with an aldehyde of structure R₂CHO. In certainembodiments, the reagent R₂CH(OMe)₂ or other acetal is formed from thecorresponding aldehyde R₂CHO. In certain embodiments, R₂ is asubstituted or unsubstituted aryl or heteroaryl moiety as described inthe classes and subclasses herein. In other embodiments, the methodsoptionally comprises additional steps of protecting and/or deprotectingfunctional groups of R₁, R₁′, R₂, or R₃. In other embodiments, themethod optionally comprises additional steps of modifying functionalgroups of R₁, R₁′, R₂, or R₃. For example, in FIG. 4 the protectedhydroxamic acid functionality of R₁′ is deprotected.

In certain embodiments, the step of providing a beta-hydroxy ketonehaving the structure:

comprises reacting an aldehyde of formula:

with a ketone of formula:

under suitable conditions (e.g., basic conditions) to form thebeta-hydroxy ketone.

In certain exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain other exemplary embodiments, the epoxy alcohol has thestructure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain other exemplary embodiments, the epoxy alcohol has thestructure:

the diol has the structure:

wherein X is S or O;

and the core scaffold has the structure:

In certain exemplary embodiments, A is a hydroxamic acid. In certainembodiments, L is an C₁-C₈ alkylidene moiety. In certain embodiments, R₃is a substituted or unsubstituted phenyl. In certain particularembodiments, R₃ is an unsubstituted phenyl. In certain embodiments, R₃is a substituted phenyl. In certain embodiments, X is O. In otherembodiments, X is S. In certain embodiments, X is NH or NR_(B). Incertain embodiments, R_(B) is substituted or unsubstituted aryl orheteroaryl.

Pharmaceutical Compositions

As discussed above, the present invention provides novel compoundshaving antitumor, antineurodegernative, antibiotic, andantiproliferative activity, and thus the inventive compounds are usefulfor the treatment of cancer, benign neoplasms, neurodegenerativedisorders, protein degradation disorders, and protein depositiondisorders.

Accordingly, in another aspect of the present invention, pharmaceuticalcompositions are provided, which comprise any one of the compoundsdescribed herein (or a prodrug, pharmaceutically acceptable salt orother pharmaceutically acceptable derivative thereof), and optionallycomprise a pharmaceutically acceptable carrier. In certain embodiments,these compositions optionally further comprise one or more additionaltherapeutic agents. Alternatively, a compound of this invention may beadministered to a patient in need thereof in combination with theadministration of one or more other therapeutic agents. For example,additional therapeutic agents for conjoint administration or inclusionin a pharmaceutical composition with a compound of this invention may bean approved chemotherapeutic agent, or it may be any one of a number ofagents undergoing approval in the Food and Drug Administration thatultimately obtain approval for the treatment of protozoal infectionsand/or any disorder associated with cellular hyperproliferation. Incertain other embodiments, the additional therapeutic agent is ananticancer agent, as discussed in more detail herein. In certain otherembodiments, the compositions of the invention are useful for thetreatment of protozoal infections. In the treatment of cancer or proteindegradation disorders, the inventive compound may be combined with aproteasome inhibitor (e.g., bortezomib, R115777 FTI, MG132, NPI-0052,etc.). In the treatment of cancer or protein degradation disorders, theinventive compound may be combined with protein degradation inhibitor(e.g., another inventive compound, a tubacin-like compound, bortezomib,R115777 FTI, MG132, NPI-0052, SAHA, ¹⁶⁶Ho-DOTMP, arsenic trioxide,17-AAG, MG132, sapojargon, etc.).

As discussed above, the compounds of the present invention are useful asanticancer agents, and thus may be useful in the treatment of cancer, byeffecting tumor cell death or inhibiting the growth of tumor cells. Ingeneral, the inventive anticancer agents are useful in the treatment ofcancers, including, but not limited to breast cancer, brain cancer, skincancer, cervical cancer, colon and rectal cancer, leukemia, lung cancer,melanoma, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer,pancreatic cancer, prostate cancer, and gastric cancer, to name a few.In certain embodiments, the inventive anticancer agents are activeagainst leukemia cells, and thus are useful for the treatment ofleukemias (e.g., myeloid, lymphocytic, promyelocytic, myelocytic andlymphoblastic leukemias, whether acute or chromic forms). In still otherembodiments, the inventive anticancer agents are active against solidtumors and also kill and/or inhibit the growth of multidrug resistantcells (MDR cells). In certain embodiments, the inventive anticanceragents are active against cancers which are resistant to other knownanti-neoplastic agents or which have been found not to respondclinically to other known anti-neoplastic agents.

It will also be appreciated that the compounds and pharmaceuticalcompositions of the present invention can be employed in combinationtherapies, that is, the compounds and pharmaceutical compositions can beadministered concurrently with, prior to, or subsequent to, one or moreother desired therapeutics or medical procedures. The particularcombination of therapies (therapeutics or procedures) to employ in acombination regimen will take into account compatibility of the desiredtherapeutics and/or procedures and the desired therapeutic effect to beachieved. It will also be appreciated that the therapies employed mayachieve a desired effect for the same disorder (for example, aninventive compound may be administered concurrently with anotheranticancer agent), or they may achieve different effects (e.g., controlof any adverse effects).

It will also be appreciated that certain of the compounds of presentinvention can exist in free form for treatment, or where appropriate, asa pharmaceutically acceptable derivative thereof. According to thepresent invention, a pharmaceutically acceptable derivative includes,but is not limited to, pharmaceutically acceptable salts, esters, saltsof such esters, or a pro-drug or other adduct or derivative of acompound of this invention which upon administration to a patient inneed is capable of providing, directly or indirectly, a compound asotherwise described herein, or a metabolite or residue thereof.

As used herein, the term “pharmaceutically acceptable salt” refers tothose salts which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswithout undue toxicity, irritation, allergic response and the like, andare commensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts of amines, carboxylic acids, and other types ofcompounds, are well known in the art. For example, S. M. Berge, et al.describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 66: 1-19 (1977), incorporated herein byreference. The salts can be prepared in situ during the final isolationand purification of the compounds of the invention, or separately byreacting a free base or free acid function with a suitable reagent, asdescribed generally below. For example, a free base function can bereacted with a suitable acid. Furthermore, where the compounds of theinvention carry an acidic moiety, suitable pharmaceutically acceptablesalts thereof may, include metal salts such as alkali metal salts, e.g.sodium or potassium salts; and alkaline earth metal salts, e.g. calciumor magnesium salts. Examples of pharmaceutically acceptable, nontoxicacid addition salts are salts of an amino group formed with inorganicacids such as hydrochloric acid, hydrobromic acid, phosphoric acid,sulfuric acid and perchloric acid or with organic acids such as aceticacid, oxalic acid, maleic acid, tartaric acid, citric acid, succinicacid or malonic acid or by using other methods used in the art such asion exchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hernisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Representative alkali or alkaline earth metal salts includesodium, lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, loweralkyl sulfonate and aryl sulfonate.

Additionally, as used herein, the term “pharmaceutically acceptableester” refers to esters that hydrolyze in vivo and include those thatbreak down readily in the human body to leave the parent compound or asalt thereof. Suitable ester groups include, for example, those derivedfrom pharmaceutically acceptable aliphatic carboxylic acids,particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, inwhich each alkyl or alkenyl moeity advantageously has not more than 6carbon atoms. Examples of particular esters include formates, acetates,propionates, butyrates, acrylates and ethylsuccinates.

Furthermore, the term “pharmaceutically acceptable prodrugs” as usedherein refers to those prodrugs of the compounds of the presentinvention which are, within the scope of sound medical judgment,suitable for use in contact with the issues of humans and lower animalswith undue toxicity, irritation, allergic response, and the like,commensurate with a reasonable benefit/risk ratio, and effective fortheir intended use, as well as the zwitterionic forms, where possible,of the compounds of the invention. The term “prodrug” refers tocompounds that are rapidly transformed in vivo to yield the parentcompound of the above formula, for example by hydrolysis in blood. Athorough discussion is provided in T. Higuchi and V. Stella, Pro-drugsas Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series, andin Edward B. Roche, ed., Bioreversible Carriers in Drug Design, AmericanPharmaceutical Association and Pergamon Press, 1987, both of which areincorporated herein by reference.

As described above, the pharmaceutical compositions of the presentinvention additionally comprise a pharmaceutically acceptable carrier,which, as used herein, includes any and all solvents, diluents, or otherliquid vehicle, dispersion or suspension aids, surface active agents,isotonic agents, thickening or emulsifying agents, preservatives, solidbinders, lubricants and the like, as suited to the particular dosageform desired. Remington's Pharmaceutical Sciences, Sixteenth Edition, E.W. Martin (Mack Publishing Co., Easton, Pa., 1980) discloses variouscarriers used in formulating pharmaceutical compositions and knowntechniques for the preparation thereof. Except insofar as anyconventional carrier medium is incompatible with the compounds of theinvention, such as by producing any undesirable biological effect orotherwise interacting in a deleterious manner with any othercomponent(s) of the pharmaceutical composition, its use is contemplatedto be within the scope of this invention. Some examples of materialswhich can serve as pharmaceutically acceptable carriers include, but arenot limited to, sugars such as lactose, glucose and sucrose; starchessuch as corn starch and potato starch; cellulose and its derivativessuch as sodium carboxymethyl cellulose, ethyl cellulose and celluloseacetate; powdered tragacanth; malt; gelatine; talc; excipients such ascocoa butter and suppository waxes; oils such as peanut oil, cottonseedoil; safflower oil, sesame oil; olive oil; corn oil and soybean oil;glycols; such as propylene glycol; esters such as ethyl oleate and ethyllaurate; agar; buffering agents such as magnesium hydroxide and aluminumhydroxide; alginic acid; pyrogenfree water; isotonic saline; Ringer'ssolution; ethyl alcohol, and phosphate buffer solutions, as well asother non-toxic compatible lubricants such as sodium lauryl sulfate andmagnesium stearate, as well as coloring agents, releasing agents,coating agents, sweetening, flavoring and perfuming agents,preservatives and antioxidants can also be present in the composition,according to the judgment of the formulator.

Liquid dosage forms for oral administration include, but are not limitedto, pharmaceutically acceptable emulsions, microemulsions, solutions,suspensions, syrups and elixirs. In addition to the active compounds,the liquid dosage forms may contain inert diluents commonly used in theart such as, for example, water or other solvents, solubilizing agentsand emulsifiers such as ethyl alcohol, isopropyl alcohol, ethylcarbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butylene glycol, dimethylformamide, oils (in particular,cottonseed, groundnut, corn, germ, olive, castor, and sesame oils),glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fattyacid esters of sorbitan, and mixtures thereof. Besides inert diluents,the oral compositions can also include adjuvants such as wetting agents,emulsifying and suspending agents, sweetening, flavoring, and perfumingagents.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions may be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation may also be a sterile injectablesolution, suspension or emulsion in a nontoxic parenterally acceptablediluent or solvent, for example, as a solution in 1,3-butanediol. Amongthe acceptable vehicles and solvents that may be employed are water,Ringer's solution, U.S.P. and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium prior to use.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This may be accomplished by the use of a liquid suspension orcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolutionthat, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform is accomplished by dissolving or suspending the drug in an oilvehicle. Injectable depot forms are made by forming microencapsulematrices of the drug in biodegradable polymers such aspolylactide-polyglycolide. Depending upon the ratio of drug to polymerand the nature of the particular polymer employed, the rate of drugrelease can be controlled. Examples of other biodegradable polymersinclude (poly(orthoesters) and poly(anhydrides). Depot injectableformulations are also prepared by entrapping the drug in liposomes ormicroemulsions which are compatible with body tissues.

Compositions for rectal or vaginal administration are preferablysuppositories which can be prepared by mixing the compounds of thisinvention with suitable non-irritating excipients or carriers such ascocoa butter, polyethylene glycol or a suppository wax which are solidat ambient temperature but liquid at body temperature and therefore meltin the rectum or vaginal cavity and release the active compound.

Solid dosage forms for oral administration include capsules, tablets,pills, powders, and granules. In such solid dosage forms, the activecompound is mixed with at least one inert, pharmaceutically acceptableexcipient or carrier such as sodium citrate or dicalcium phosphateand/or a) fillers or extenders such as starches, lactose, sucrose,glucose, mannitol, and silicic acid, b) binders such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone,sucrose, and acacia, c) humectants such as glycerol, d) disintegratingagents such as agar-agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, e) solutionretarding agents such as paraffin, f) absorption accelerators such asquaternary ammonium compounds, g) wetting agents such as, for example,cetyl alcohol and glycerol monostearate, h) absorbents such as kaolinand bentonite clay, and i) lubricants such as talc, calcium stearate,magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate,and mixtures thereof. In the case of capsules, tablets and pills, thedosage form may also comprise buffering agents.

Solid compositions of a similar type may also be employed as fillers insoft and hard-filled gelatin capsules using such excipients as lactoseor milk sugar as well as high molecular weight polyethylene glycols andthe like. The solid dosage forms of tablets, dragees, capsules, pills,and granules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the pharmaceutical formulatingart. They may optionally contain opacifying agents and can also be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of embedding compositions that can be usedinclude polymeric substances and waxes. Solid compositions of a similartype may also be employed as fillers in soft and hard-filled gelatincapsules using such excipients as lactose or milk sugar as well as highmolecular weight polyethylene glycols and the like.

The active compounds can also be in micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active compound may be admixed with at least one inertdiluent such as sucrose, lactose and starch. Such dosage forms may alsocomprise, as in normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such asmagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may also comprisebuffering agents. They may optionally contain opacifying agents and canalso be of a composition that they release the active ingredient(s)only, or preferentially, in a certain part of the intestinal tract,optionally, in a delayed manner. Examples of embedding compositionswhich can be used include polymeric substances and waxes.

The present invention encompasses pharmaceutically acceptable topicalformulations of inventive compounds. The term “pharmaceuticallyacceptable topical formulation,” as used herein, means any formulationwhich is pharmaceutically acceptable for intradermal administration of acompound of the invention by application of the formulation to theepidermis. In certain embodiments of the invention, the topicalformulation comprises a carrier system. Pharmaceutically effectivecarriers include, but are not limited to, solvents (e.g., alcohols, polyalcohols, water), creams, lotions, ointments, oils, plasters, liposomes,powders, emulsions, microemulsions, and buffered solutions (e.g.,hypotonic or buffered saline) or any other carrier known in the art fortopically administering pharmaceuticals. A more complete listing ofart-known carriers is provided by reference texts that are standard inthe art, for example, Remington's Pharmaceutical Sciences, 16th Edition,1980 and 17th Edition, 1985, both published by Mack Publishing Company,Easton, Pa., the disclosures of which are incorporated herein byreference in their entireties. In certain other embodiments, the topicalformulations of the invention may comprise excipients. Anypharmaceutically acceptable excipient known in the art may be used toprepare the inventive pharmaceutically acceptable topical formulations.Examples of excipients that can be included in the topical formulationsof the invention include, but are not limited to, preservatives,antioxidants, moisturizers, emollients, buffering agents, solubilizingagents, other penetration agents, skin protectants, surfactants, andpropellants, and/or additional therapeutic agents used in combination tothe inventive compound. Suitable preservatives include, but are notlimited to, alcohols, quaternary amines, organic acids, parabens, andphenols. Suitable antioxidants include, but are not limited to, ascorbicacid and its esters, sodium bisulfite, butylated hydroxytoluene,butylated hydroxyanisole, tocopherols, and chelating agents like EDTAand citric acid. Suitable moisturizers include, but are not limited to,glycerine, sorbitol, polyethylene glycols, urea, and propylene glycol.Suitable buffering agents for use with the invention include, but arenot limited to, citric, hydrochloric, and lactic acid buffers. Suitablesolubilizing agents include, but are not limited to, quaternary ammoniumchlorides, cyclodextrins, benzyl benzoate, lecithin, and polysorbates.Suitable skin protectants that can be used in the topical formulationsof the invention include, but are not limited to, vitamin E oil,allatoin, dimethicone, glycerin, petrolatum, and zinc oxide.

In certain embodiments, the pharmaceutically acceptable topicalformulations of the invention comprise at least a compound of theinvention and a penetration enhancing agent. The choice of topicalformulation will depend or several factors, including the condition tobe treated, the physicochemical characteristics of the inventivecompound and other excipients present, their stability in theformulation, available manufacturing equipment, and costs constraints.As used herein the term “penetration enhancing agent” means an agentcapable of transporting a pharmacologically active compound through thestratum corneum and into the epidermis or dermis, preferably, withlittle or no systemic absorption. A wide variety of compounds have beenevaluated as to their effectiveness in enhancing the rate of penetrationof drugs through the skin. See, for example, Percutaneous PenetrationEnhancers, Maibach H. I. and Smith H. E. (eds.), CRC Press, Inc., BocaRaton, Fla. (1995), which surveys the use and testing of various skinpenetration enhancers, and Buyuktimkin et al., Chemical Means ofTransdermal Drug Permeation Enhancement in Transdermal and Topical DrugDelivery Systems, Gosh T. K., Pfister W. R., Yum S. I. (Eds.),Interpharm Press Inc., Buffalo Grove, Ill. (1997). In certain exemplaryembodiments, penetration agents for use with the invention include, butare not limited to, triglycerides (e.g., soybean oil), aloe compositions(e.g., aloe-vera gel), ethyl alcohol, isopropyl alcohol,octolyphenylpolyethylene glycol, oleic acid, polyethylene glycol 400,propylene glycol, N-decylmethylsulfoxide, fatty acid esters (e.g.,isopropyl myristate, methyl laurate, glycerol monooleate, and propyleneglycol monooleate) and N-methylpyrrolidone.

In certain embodiments, the compositions may be in the form ofointments, pastes, creams, lotions, gels, powders, solutions, sprays,inhalants or patches. In certain exemplary embodiments, formulations ofthe compositions according to the invention are creams, which mayfurther contain saturated or unsaturated fatty acids such as stearicacid, palmitic acid, oleic acid, palmito-oleic acid, cetyl or oleylalcohols, stearic acid being particularly preferred. Creams of theinvention may also contain a non-ionic surfactant, for example,polyoxy-40-stearate. In certain embodiments, the active component isadmixed under sterile conditions with a pharmaceutically acceptablecarrier and any needed preservatives or buffers as may be required.Ophthalmic formulation, eardrops, and eye drops are also contemplated asbeing within the scope of this invention. Additionally, the presentinvention contemplates the use of transdermal patches, which have theadded advantage of providing controlled delivery of a compound to thebody. Such dosage forms are made by dissolving or dispensing thecompound in the proper medium. As discussed above, penetration enhancingagents can also be used to increase the flux of the compound across theskin. The rate can be controlled by either providing a rate controllingmembrane or by dispersing the compound in a polymer matrix or gel.

It will also be appreciated that the compounds and pharmaceuticalcompositions of the present invention can be formulated and employed incombination therapies, that is, the compounds and pharmaceuticalcompositions can be formulated with or administered concurrently with,prior to, or subsequent to, one or more other desired therapeutics ormedical procedures. The particular combination of therapies(therapeutics or procedures) to employ in a combination regimen willtake into account compatibility of the desired therapeutics and/orprocedures and the desired therapeutic effect to be achieved. It willalso be appreciated that the therapies employed may achieve a desiredeffect for the same disorder (for example, an inventive compound may beadministered concurrently with another immunomodulatory agent,anticancer agent or agent useful for the treatment of psoriasis), orthey may achieve different effects (e.g., control of any adverseeffects).

For example, other therapies or anticancer agents that may be used incombination with the inventive compounds of the present inventioninclude surgery, radiotherapy (in but a few examples, γ-radiation,neutron beam radiotherapy, electron beam radiotherapy, proton therapy,brachytherapy, and systemic radioactive isotopes, to name a few),endocrine therapy, biologic response modifiers (interferons,interleukins, and tumor necrosis factor (TNF) to name a few),hyperthermia and cryotherapy, agents to attenuate any adverse effects(e.g., antiemetics), and other approved chemotherapeutic drugs,including, but not limited to, alkylating drugs (e.g., mechlorethamine,chlorambucil, Cyclophosphamide, Melphalan, Ifosfamide), antimetabolites(e.g., Methotrexate), purine antagonists and pyrimidine antagonists(e.g., 6-Mercaptopurine, 5-Fluorouracil, Cytarabile, Gemcitabine),spindle poisons (e.g., Vinblastine, Vincristine, Vinorelbine,Paclitaxel), podophyllotoxins (e.g., Etoposide, Irinotecan, Topotecan),antibiotics (Doxorubicin, Bleomycin, Mitomycin), nitrosoureas (e.g.,Carmustine, Lomustine), inorganic ions (e.g., Cisplatin, Carboplatin),enzymes (e.g., Asparaginase), and hormones (e.g., Tamoxifen, Leuprolide,Flutamide, and Megestrol), to name a few. For a more comprehensivediscussion of updated cancer therapies see, The Merck Manual,Seventeenth Ed. 1999, the entire contents of which are herebyincorporated by reference. See also the National Cancer Institute (CNI)website (www.nci.nih.gov) and the Food and Drug Administration (FDA)website for a list of the FDA approved oncology drugs(www.fda.gov/cder/cancer/druglistframe).

In certain embodiments, the pharmaceutical compositions of the presentinvention further comprise one or more additional therapeutically activeingredients (e.g., chemotherapeutic and/or palliative). For purposes ofthe invention, the term “palliative” refers to treatment that is focusedon the relief of symptoms of a disease and/or side effects of atherapeutic regimen, but is not curative. For example, palliativetreatment encompasses painkillers, antinausea medications,anti-pyretics, and anti-sickness drugs. In addition, chemotherapy,radiotherapy and surgery can all be used palliatively (that is, toreduce symptoms without going for cure; e.g., for shrinking tumors andreducing pressure, bleeding, pain and other symptoms of cancer).

Additionally, the present invention provides pharmaceutically acceptablederivatives of the inventive compounds, and methods of treating asubject using these compounds, pharmaceutical compositions thereof, oreither of these in combination with one or more additional therapeuticagents.

It will also be appreciated that certain of the compounds of presentinvention can exist in free form for treatment, or where appropriate, asa pharmaceutically acceptable derivative thereof. According to thepresent invention, a pharmaceutically acceptable derivative includes,but is not limited to, pharmaceutically acceptable salts, esters, saltsof such esters, or a prodrug or other adduct or derivative of a compoundof this invention which upon administration to a patient in need iscapable of providing, directly or indirectly, a compound as otherwisedescribed herein, or a metabolite or residue thereof.

Research Uses, Pharmaceutical Uses and Methods of Treatment ResearchUses

According to the present invention, the inventive compounds may beassayed in any of the available assays known in the art for identifyingcompounds having antiprotozoal, HDAC inhibitory, TDAC inhibitory,aggresome inhibitory, and/or antiproliferative activity. For example,the assay may be cellular or non-cellular, in vivo or in vitro, high- orlow-throughput format, etc.

Thus, in one aspect, compounds of this invention which are of particularinterest include those which:

-   -   exhibit HDAC-inhibitory activity;    -   exhibit TDAC-inhibitory activity;    -   exhibit HDAC Class I inhibitory activity (e.g., HDAC1, HDAC2,        HDAC3, HDAC8);    -   exhibit HDAC Class II inhibitory activity (e.g., HDAC4, HDAC5,        HDAC6, HDAC7, HDAC9a, HDAC9b, HDRP/HDAC9c, HDAC10);    -   exhibit HDAC Class IV inhibitory activity;    -   exhibit the ability to inhibit HDAC1 (Genbank Accession No.        NP_(—)004955, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC2 (Genbank Accession No.        NP_(—)001518, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC3 (Genbank Accession No.        O15739, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC4 (Genbank Accession No.        AAD29046, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC5 (Genbank Accession No.        NP_(—)005465, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC6 (Genbank Accession No.        NP_(—)006035, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC7 (Genbank Accession No.        AAP63491, incorporated herein by reference);    -   exhibit the ability to inhibit HDAC8 (Genbank Accession No.        AAF73428, NM_(—)018486, AF245664, AF230097, each of which is        incorporated herein by reference);    -   exhibit the ability to inhibit HDAC9 (Genbank Accession No.        NM_(—)178425, NM_(—)178423, NM_(—)058176, NM_(—)014707,        BC111735, NM_(—)058177, each of which is incorporated herein by        reference)    -   exhibit the ability to inhibit HDAC10 (Genbank Accession No.        NM_(—)032019, incorporated herein by reference)    -   exhibit the ability to inhibit HDAC11 (Genbank Accession No.        BC009676, incorporated herein by reference);    -   exhibit the ability to modulate the glucose-sensitive subset of        genes downstream of Ure2p;    -   exhibit the ability to inhibit the degradation of protein by the        aggresome;    -   exhibit cytotoxic or growth inhibitory effect on cancer cell        lines maintained in vitro or in animal studies using a        scientifically acceptable cancer cell xenograft model; and/or    -   exhibit a therapeutic profile (e.g., optimum safety and curative        effect) that is superior to existing chemotherapeutic agents.

As detailed in the exemplification herein, in assays to determine theability of compounds to inhibit cancer cell growth certain inventivecompounds may exhibit IC₅₀ values ≦100 μM. In certain other embodiments,inventive compounds exhibit IC₅₀ values ≦50 μM. In certain otherembodiments, inventive compounds exhibit IC₅₀ values ≦40 μM. In certainother embodiments, inventive compounds exhibit IC₅₀ values ≦30 μM. Incertain other embodiments, inventive compounds exhibit IC₅₀ values ≦20μM. In certain other embodiments, inventive compounds exhibit IC₅₀values ≦10 μM. In certain other embodiments, inventive compounds exhibitIC₅₀ values ≦7.5 μM. In certain embodiments, inventive compounds exhibitIC₅₀ values ≦5 μM. In certain other embodiments, inventive compoundsexhibit IC₅₀ values ≦2.5 μM. In certain embodiments, inventive compoundsexhibit IC₅₀ values ≦1 μM. In certain embodiments, inventive compoundsexhibit IC₅₀ values ≦0.75 μM. In certain embodiments, inventivecompounds exhibit IC₅₀ values ≦0.5 μM. In certain embodiments, inventivecompounds exhibit IC₅₀ values ≦0.25 μM. In certain embodiments,inventive compounds exhibit IC₅₀ values ≦0.1 μM. In certain otherembodiments, inventive compounds exhibit IC₅₀ values ≦75 nM. In certainother embodiments, inventive compounds exhibit IC₅₀ values ≦50 nM. Incertain other embodiments, inventive compounds exhibit IC₅₀ values ≦25nM. In certain other embodiments, inventive compounds exhibit IC₅₀values ≦10 nM. In other embodiments, exemplary compounds exhibited IC₅₀values ≦7.5 nM. In other embodiments, exemplary compounds exhibited IC₅₀values ≦5 nM.

Pharmaceutical Uses and Methods of Treatment

In general, methods of using the compounds of the present inventioncomprise administering to a subject in need thereof a therapeuticallyeffective amount of a compound of the present invention. As discussedabove, the compounds of the invention are selective inhibitors ofhistone deacetylases and, as such, are useful in the treatment ofdisorders modulated by histone deacetylases. As discussed above, thecompounds of the invention are selective inhibitors of tubulindeacetylases and, as such, are useful in the treatment of disordersmodulated by tubulin deacetylases. For example, compounds of theinvention may be useful in the treatment of cancer (e.g., breast cancer,prostate cancer, multiple myeloma, leukemia, lymphoma, etc.).Accordingly, in yet another aspect, according to the methods oftreatment of the present invention, tumor cells are killed, or theirgrowth is inhibited by contacting said tumor cells with an inventivecompound or composition, as described herein.

Thus, in another aspect of the invention, methods for the treatment ofcancer are provided comprising administering a therapeutically effectiveamount of an inventive compound, as described herein, to a subject inneed thereof. In certain embodiments, a method for the treatment ofcancer is provided comprising administering a therapeutically effectiveamount of an inventive compound, or a pharmaceutical compositioncomprising an inventive compound to a subject in need thereof, in suchamounts and for such time as is necessary to achieve the desired result.In certain embodiments of the present invention a “therapeuticallyeffective amount” of the inventive compound or pharmaceuticalcomposition is that amount effective for killing or inhibiting thegrowth of tumor cells. The compounds and compositions, according to themethod of the present invention, may be administered using any amountand any route of administration effective for killing or inhibiting thegrowth of tumor cells. Thus, the expression “amount effective to kill orinhibit the growth of tumor cells,” as used herein, refers to asufficient amount of agent to kill or inhibit the growth of tumor cells.The exact amount required will vary from subject to subject, dependingon the species, age, and general condition of the subject, the severityof the infection, the particular anticancer agent, its mode ofadministration, and the like.

In certain embodiments, the method involves the administration of atherapeutically effective amount of the compound or a pharmaceuticallyacceptable derivative thereof to a subject (including, but not limitedto a human or animal) in need of it. In certain embodiments, theinventive compounds as useful for the treatment of cancer (including,but not limited to, glioblastoma, retinoblastoma, breast cancer,cervical cancer, colon and rectal cancer, leukemia (e.g., CML, AML, CLL,ALL), lymphoma, lung cancer (including, but not limited to small celllung cancer), melanoma and/or skin cancer, multiple myeloma,non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostatecancer and gastric cancer, bladder cancer, uterine cancer, kidneycancer, testicular cancer, stomach cancer, brain cancer, liver cancer,or esophageal cancer).

In certain embodiments, the inventive anticancer agents are useful inthe treatment of cancers and other proliferative disorders, including,but not limited to breast cancer, cervical cancer, colon and rectalcancer, leukemia, lung cancer, melanoma, multiple myeloma, non-Hodgkin'slymphoma, ovarian cancer, pancreatic cancer, prostate cancer, andgastric cancer, to name a few. In certain embodiments, the inventiveanticancer agents are active against leukemia cells and melanoma cells,and thus are useful for the treatment of leukemias (e.g., myeloid,lymphocytic, myelocytic and lymphoblastic leukemias) and malignantmelanomas. In still other embodiments, the inventive anticancer agentsare active against solid tumors.

In certain embodiments, the inventive compounds also find use in theprevention of restenosis of blood vessels subject to traumas such asangioplasty and stenting. For example, it is contemplated that thecompounds of the invention will be useful as a coating for implantedmedical devices, such as tubings, shunts, catheters, artificialimplants, pins, electrical implants such as pacemakers, and especiallyfor arterial or venous stents, including balloon-expandable stents. Incertain embodiments inventive compounds may be bound to an implantablemedical device, or alternatively, may be passively adsorbed to thesurface of the implantable device. In certain other embodiments, theinventive compounds may be formulated to be contained within, or,adapted to release by a surgical or medical device or implant, such as,for example, stents, sutures, indwelling catheters, prosthesis, and thelike. For example, drugs having antiproliferative and anti-inflammatoryactivities have been evaluated as stent coatings, and have shown promisein preventing restenosis (See, for example, Presbitero P. et al., “Drugeluting stents do they make the difference?”, Minerva Cardioangiol,2002, 50(5):431-442; Ruygrok P. N. et al., “Rapamycin in cardiovascularmedicine”, Intern. Med. J., 2003, 33(3):103-109; and Marx S. O. et al.,“Bench to bedside: the development of rapamycin and its application tostent restenosis”, Circulation, 2001, 104(8):852-855, each of thesereferences is incorporated herein by reference in its entirety).Accordingly, without wishing to be bound to any particular theory,Applicant proposes that inventive compounds having antiproliferativeeffects can be used as stent coatings and/or in stent drug deliverydevices, inter alia for the prevention of restenosis or reduction ofrestenosis rate. Suitable coatings and the general preparation of coatedimplantable devices are described in U.S. Pat. Nos. 6,099,562;5,886,026; and 5,304,121; each of which is incorporated herein byreference. The coatings are typically biocompatible polymeric materialssuch as a hydrogel polymer, polymethyldisiloxane, polycaprolactone,polyethylene glycol, polylactic acid, ethylene vinyl acetate, andmixtures thereof. The coatings may optionally be further covered by asuitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol,phospholipids or combinations thereof to impart controlled releasecharacteristics in the composition. A variety of compositions andmethods related to stent coating and/or local stent drug delivery forpreventing restenosis are known in the art (see, for example, U.S. Pat.Nos. 6,517,889; 6,273,913; 6,258,121; 6,251,136; 6,248,127; 6,231,600;6,203,551; 6,153,252; 6,071,305; 5,891,507; 5,837,313 and published U.S.patent application No.: US2001/0027340, each of which is incorporatedherein by reference in its entirety). For example, stents may be coatedwith polymer-drug conjugates by dipping the stent in polymer-drugsolution or spraying the stent with such a solution. In certainembodiment, suitable materials for the implantable device includebiocompatible and nontoxic materials, and may be chosen from the metalssuch as nickel-titanium alloys, steel, or biocompatible polymers,hydrogels, polyurethanes, polyethylenes, ethylenevinyl acetatecopolymers, etc. In certain embodiments, the inventive compound iscoated onto a stent for insertion into an artery or vein followingballoon angioplasty.

The compounds of this invention or pharmaceutically acceptablecompositions thereof may also be incorporated into compositions forcoating implantable medical devices, such as prostheses, artificialvalves, vascular grafts, stents and catheters. Accordingly, the presentinvention, in another aspect, includes a composition for coating animplantable device comprising a compound of the present invention asdescribed generally above, and in classes and subclasses herein, and acarrier suitable for coating said implantable device. In still anotheraspect, the present invention includes an implantable device coated witha composition comprising a compound of the present invention asdescribed generally above, and in classes and subclasses herein, and acarrier suitable for coating said implantable device.

Within other aspects of the present invention, methods are provided forexpanding the lumen of a body passageway, comprising inserting a stentinto the passageway, the stent having a generally tubular structure, thesurface of the structure being coated with (or otherwise adapted torelease) an inventive compound or composition, such that the passagewayis expanded. In certain embodiments, the lumen of a body passageway isexpanded in order to eliminate a biliary, gastrointestinal, esophageal,tracheal/bronchial, urethral and/or vascular obstruction.

Methods for eliminating biliary, gastrointestinal, esophageal,tracheal/bronchial, urethral and/or vascular obstructions using stentsare known in the art. The skilled practitioner will know how to adaptthese methods in practicing the present invention. For example, guidancecan be found in U.S. Patent Publication No.: 2003/0004209 in paragraphs[0146]-[0155], which paragraphs are hereby incorporated herein byreference.

Another aspect of the invention relates to a method for inhibiting thegrowth of multidrug resistant cells in a biological sample or a patient,which method comprises administering to the patient, or contacting saidbiological sample with a compound of the invention or a compositioncomprising said compound.

Additionally, the present invention provides pharmaceutically acceptablederivatives of the inventive compounds, and methods of treating asubject using these compounds, pharmaceutical compositions thereof, oreither of these in combination with one or more additional therapeuticagents.

Another aspect of the invention relates to a method of treating orlessening the severity of a disease or condition associated with aproliferation disorder in a patient, said method comprising a step ofadministering to said patient, a compound of formula I or a compositioncomprising said compound.

It will be appreciated that the compounds and compositions, according tothe method of the present invention, may be administered using anyamount and any route of administration effective for the treatment ofcancer and/or disorders associated with cell hyperproliferation. Forexample, when using the inventive compounds for the treatment of cancer,the expression “effective amount” as used herein, refers to a sufficientamount of agent to inhibit cell proliferation, or refers to a sufficientamount to reduce the effects of cancer. The exact amount required willvary from subject to subject, depending on the species, age, and generalcondition of the subject, the severity of the diseases, the particularanticancer agent, its mode of administration, and the like.

The compounds of the invention are preferably formulated in dosage unitform for ease of administration and uniformity of dosage. The expression“dosage unit form” as used herein refers to a physically discrete unitof therapeutic agent appropriate for the patient to be treated. It willbe understood, however, that the total daily usage of the compounds andcompositions of the present invention will be decided by the attendingphysician within the scope of sound medical judgment. The specifictherapeutically effective dose level for any particular patient ororganism will depend upon a variety of factors including the disorderbeing treated and the severity of the disorder; the activity of thespecific compound employed; the specific composition employed; the age,body weight, general health, sex and diet of the patient; the time ofadministration, route of administration, and rate of excretion of thespecific compound employed; the duration of the treatment; drugs used incombination or coincidental with the specific compound employed; andlike factors well known in the medical arts (see, for example, Goodmanand Gilman's, “The Pharmacological Basis of Therapeutics”, TenthEdition, A. Gilman, J. Hardman and L. Limbird, eds., McGraw-Hill Press,155-173, 2001, which is incorporated herein by reference in itsentirety).

Another aspect of the invention relates to a method for inhibitinghistone deacetylase activity in a biological sample or a patient, whichmethod comprises administering to the patient, or contacting saidbiological sample with a compound of formula I or a compositioncomprising said compound.

Furthermore, after formulation with an appropriate pharmaceuticallyacceptable carrier in a desired dosage, the pharmaceutical compositionsof this invention, can be administered to humans and other animalsorally, rectally, parenterally, intracisternally, intravaginally,intraperitoneally, topically (as by powders, ointments, creams ordrops), bucally, as an oral or nasal spray, or the like, depending onthe severity of the infection being treated. In certain embodiments, thecompounds of the invention may be administered at dosage levels of about0.001 mg/kg to about 50 mg/kg, from about 0.01 mg/kg to about 25 mg/kg,or from about 0.1 mg/kg to about 10 mg/kg of subject body weight perday, one or more times a day, to obtain the desired therapeutic effect.It will also be appreciated that dosages smaller than 0.001 mg/kg orgreater than 50 mg/kg (for example 50-100 mg/kg) can be administered toa subject. In certain embodiments, compounds are administered orally orparenterally.

Treatment Kit

In other embodiments, the present invention relates to a kit forconveniently and effectively carrying out the methods in accordance withthe present invention. In general, the pharmaceutical pack or kitcomprises one or more containers filled with one or more of theingredients of the pharmaceutical compositions of the invention. Suchkits are especially suited for the delivery of solid oral forms such astablets or capsules. Such a kit preferably includes a number of unitdosages, and may also include a card having the dosages oriented in theorder of their intended use. If desired, a memory aid can be provided,for example in the form of numbers, letters, or other markings or with acalendar insert, designating the days in the treatment schedule in whichthe dosages can be administered. Alternatively, placebo dosages, orcalcium dietary supplements, either in a form similar to or distinctfrom the dosages of the pharmaceutical compositions, can be included toprovide a kit in which a dosage is taken every day. Optionallyassociated with such container(s) can be a notice in the form prescribedby a governmental agency regulating the manufacture, use or sale ofpharmaceutical products, which notice reflects approval by the agency ofmanufacture, use or sale for human administration.

EQUIVALENTS

The representative examples which follow are intended to help illustratethe invention, and are not intended to, nor should they be construed to,limit the scope of the invention. Indeed, various modifications of theinvention and many further embodiments thereof, in addition to thoseshown and described herein, will become apparent to those skilled in theart from the full contents of this document, including the exampleswhich follow and the references to the scientific and patent literaturecited herein. It should further be appreciated that, unless otherwiseindicated, the entire contents of each of the references cited hereinare incorporated herein by reference to help illustrate the state of theart. The following examples contain important additional information,exemplification and guidance which can be adapted to the practice ofthis invention in its various embodiments and the equivalents thereof.

These and other aspects of the present invention will be furtherappreciated upon consideration of the following Examples, which areintended to illustrate certain particular embodiments of the inventionbut are not intended to limit its scope, as defined by the claims.

EXAMPLES

The compounds of this invention and their preparation can be understoodfurther by the examples that illustrate some of the processes by whichthese compounds are prepared or used. It will be appreciated, however,that these examples do not limit the invention. Variations of theinvention, now known or further developed, are considered to fall withinthe scope of the present invention as described herein and ashereinafter claimed.

Example 1 Synthetic Methods

The various references cited herein provide helpful backgroundinformation on preparing compounds similar to the inventive compoundsdescribed herein or relevant intermediates, as well as information onformulation, uses, and administration of such compounds which may be ofinterest.

Moreover, the practitioner is directed to the specific guidance andexamples provided in this document relating to various exemplarycompounds and intermediates thereof.

The compounds of this invention and their preparation can be understoodfurther by the examples that illustrate some of the processes by whichthese compounds are prepared or used. It will be appreciated, however,that these examples do not limit the invention. Variations of theinvention, now known or further developed, are considered to fall withinthe scope of the present invention as described herein and ashereinafter claimed.

According to the present invention, any available techniques can be usedto make or prepare the inventive compounds or compositions includingthem. For example, a variety of a variety combinatorial techniques,parallel synthesis and/or solid phase synthetic methods such as thosediscussed in detail below may be used. Alternatively or additionally,the inventive compounds may be prepared using any of a variety ofsolution phase synthetic methods known in the art.

It will be appreciated as described below, that a variety of inventivecompounds can be synthesized according to the methods described herein.The starting materials and reagents used in preparing these compoundsare either available from commercial suppliers such as Aldrich ChemicalCompany (Milwaukee, Wis.), Bachem (Torrance, Calif.), Sigma (St. Louis,Mo.), or are prepared by methods well known to a person of ordinaryskill in the art following procedures described in such references asFieser and Fieser 1991, “Reagents for Organic Synthesis”, vols 1-17,John Wiley and Sons, New York, N.Y., 1991; Rodd 1989 “Chemistry ofCarbon Compounds”, vols. 1-5 and supps, Elsevier Science Publishers,1989; “Organic Reactions”, vols 1-40, John Wiley and Sons, New York,N.Y., 1991; March 2001, “Advanced Organic Chemistry”, 5th ed. John Wileyand Sons, New York, N.Y.; and Larock 1990, “Comprehensive OrganicTransformations: A Guide to Functional Group Preparations”, 2^(nd) ed.VCH Publishers. These schemes are merely illustrative of some methods bywhich the compounds of this invention can be synthesized, and variousmodifications to these schemes can be made and will be suggested to aperson of ordinary skill in the art having regard to this disclosure.

The starting materials, intermediates, and compounds of this inventionmay be isolated and purified using conventional techniques, includingfiltration, distillation, crystallization, chromatography, and the like.They may be characterized using conventional methods, including physicalconstants and spectral data.

Example 2 Biological Assay Procedures

Cell culture and Transfections. TAg-Jurkat cells were transfected byelectroporation with 5 μg of FLAG-epitope-tagged pBJ5 constructs forexpression of recombinant proteins. Cells were harvested 48 hposttransfection.

HDAC assays. [³H]Acetate-incorporated histones were isolated frombutyrate-treated HeLa cells by hydroxyapatite chromatography (asdescribed in Tong, et al. Nature 1997, 395, 917-921) Immunoprecipitateswere incubated with 1.4 μg (10,000 dpm) histones for 3 h at 37° C. HDACactivity was determined by scintillation counting of the ethylacetate-soluble [³H]acetic acid (as described in Taunton, et al.,Science 1996, 272, 408-411). Compounds were added in DMSO such thatfinal assay concentrations were 1% DMSO. IC₅₀s were calculated usingPrism 3.0 software. Curve fitting was done without constraints using theprogram's Sigmoidal-Dose Response parameters. All data points wereacquired in duplicate and IC50s are calculated from the compositeresults of at least two separate experiments.

Example 3 In Vivo Activity

Although a variety of methods can be utilized, one exemplary method bywhich the in vivo activity of the inventive compounds is determined isby subcutaneously transplanting a desired tumor mass in mice. Drugtreatment is then initiated when tumor mass reaches approximately 100 nmafter transplantation of the tumor mass. A suitable composition, asdescribed in more detail above, is then administered to the mice,preferably in saline and also preferably administered once a day atdoses of 5, 10 and 25 mg/kg, although it will be appreciated that otherdoses can also be administered. Body weight and tumor size are thenmeasured daily and changes in percent ratio to initial values areplotted. In cases where the transplanted tumor ulcerates, the weightloss exceeds 25-30% of control weight loss, the tumor weight reaches 10%of the body weight of the cancer-bearing mouse, or the cancer-bearingmouse is dying, the animal is sacrificed in accordance with guidelinesfor animal welfare.

Example 4 Assays to Identify Potential Antiprotozoal Compounds byInhibition of Histone Deacetylase

As detailed in U.S. Pat. No. 6,068,987, incorporated herein byreference, inhibitors of histone deacetylases may also be useful asantiprotozoal agents. Described therein are assays for histonedeacetylase activity and inhibition and describe a variety of knownprotozoal diseases. The entire contents of U.S. Pat. No. 6,068,987 arehereby incorporated by reference.

Example 5 High-Throughput Immunofluorescence Assay

Compounds of the invention are tested from their HDAC or TDACspecificity using a high-throughput immunofluorescence-based assay. Theassay is based on the use of specific antibodies for acetylated tubulinand acetylated lysine (i.e., a marker for acetylated histones).

Cells (e.g., 293T cells) are incubated the inventive compound over atest range of concentrations after the cells have been allowed to adhereto the cell culture plate overnight. After a determined time ofincubation with the inventive compound (e.g., 6-8 hours), the cells aretreated with a first primary antibody directed against acetylatedtubulin and a second primary antibody directed against acetylatedlysine. The cells are then contacted with two secondary antibodiesspecific for each of the primary antibodies and identifiable by a uniquefluorescent signal.

The plates are then imaged, and the fluorescence signal from each of thesecondary antibodies is quantitated. The data gathered is then used tocalculate dose-response curves, to calculate IC₅₀ values, to establishstructure-function relationships, to calculate the ratio of HDAC to TDACinhibition, and to determine the specificity for HDAC or TDAC.

1. A compound of the formula:

wherein R₁ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(A); —C(═O)R_(A);—CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂;—NHC(O)R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; R₂ is hydrogen;halogen; cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(B); —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B);—SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂; —NHC(O)R_(B); or —C(R_(B))₃;wherein each occurrence of R_(B) is independently a hydrogen, aprotecting group, an aliphatic moiety, a heteroaliphatic moiety, an acylmoiety; an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio;arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; orheteroarylthio moiety; and R₃ is hydrogen; halogen; cyclic or acyclic,substituted or unsubstituted, branched or unbranched aliphatic; cyclicor acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety; and pharmaceutically acceptable salts and derivatives thereof.2. The compound of claim 1, wherein the compound is of one of theformulae:


3. The compound of claim 1, wherein R₁ is of the formula:

wherein R₁′ is

wherein Y is NH or O; L is a linker moiety; and A comprises a functionalgroup that inhibits histone or tubulin deacetylase.
 4. The compound ofclaim 3, wherein R₁ is of the formula:


5. The compound of claim 3, wherein R₁′ is

wherein n is an integer between 0 and 15, inclusive.
 6. The compound ofclaim 5, wherein n is 5 or
 6. 7. The compound of claim 1, wherein R₂ isof the formula:

wherein m is an integer between 0 and 8, inclusive; preferably, between1 and 6, inclusive; X is O, S, CH₂, NH, or NR₂′; and R₂′ is aliphatic,heteroaliphatic, acyl, substituted or unsubstituted aryl, or substitutedor unsubstituted heteroaryl.
 8. The compound of claim 7, wherein X is O.9. The compound of claim 7, wherein X is S.
 10. The compound of claim 7,wherein m is
 1. 11. The compound of claim 7, wherein R₂′ is substitutedor unsubstituted heteroaryl.
 12. The compound of claim 1, wherein R₂ isselected from one of the following:


13. The compound of claim 1, wherein R₂ is selected from one of thefollowing:


14. The compound of claim 1, wherein R₂ is

wherein X is N, and Y is NH, S, or O.
 15. The compound of claim 1,wherein R₂ is


16. The compound of claim 1, wherein R₃ is a substituted orunsubstituted aryl.
 17. The compound of claim 1, wherein R₃ is anunsubstituted phenyl moiety.
 18. The compound of claim 1, wherein R₃ isa substituted phenyl moiety.
 19. The compound of claim 1 of the formula:

wherein n is an integer between 1 and 5, inclusive; and each occurrenceof R₃′ is independently hydrogen; halogen; cyclic or acyclic,substituted or unsubstituted, branched or unbranched aliphatic; cyclicor acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety.
 20. The compound of claim 1 of the formula:


21. The compound of claim 1 of one of the formulae:


22. The compound of claim 1 of formula:


23. A compound of the formula:

wherein R₁ is hydrogen; halogen; cyclic or acyclic, substituted orunsubstituted, branched or unbranched aliphatic; cyclic or acyclic,substituted or unsubstituted, branched or unbranched heteroaliphatic;substituted or unsubstituted, branched or unbranched acyl; substitutedor unsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(A); —C(═O)R_(A);—CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —NO₂; —N(R_(A))₂;—NHC(O)R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; R₂ is hydrogen;halogen; cyclic or acyclic, substituted or unsubstituted, branched orunbranched aliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched heteroaliphatic; substituted or unsubstituted,branched or unbranched acyl; substituted or unsubstituted, branched orunbranched aryl; substituted or unsubstituted, branched or unbranchedheteroaryl; —OR_(B); —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B);—SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂; —NHC(O)R_(B); or —C(R_(B))₃;wherein each occurrence of R_(B) is independently a hydrogen, aprotecting group, an aliphatic moiety, a heteroaliphatic moiety, an acylmoiety; an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio;arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; orheteroarylthio moiety; and R₃ is hydrogen; halogen; cyclic or acyclic,substituted or unsubstituted, branched or unbranched aliphatic; cyclicor acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety; and pharmaceutically acceptable salts and derivatives thereof.24. The compound of claim 23, wherein the compound is of one of theformulae:


25. The compound of claim 23, wherein R₁ is of the formula:

wherein R₁′ is

wherein Y is NH or O; L is a linker moiety; and A comprises a functionalgroup that inhibits histone or tubulin deacetylase.
 26. The compound ofclaim 25, wherein R₁ is of the formula:


27. The compound of claim 25, wherein R₁′ is

wherein n is an integer between 0 and 15, inclusive.
 28. The compound ofclaim 27, wherein n is 5 or
 6. 29. The compound of claim 23, wherein R₂is of the formula:

wherein m is an integer between 0 and 8, inclusive; preferably, between1 and 6, inclusive; X is O, S, CH₂, NH, or NR₂′; and R₂′ is aliphatic,heteroaliphatic, acyl, substituted or unsubstituted aryl, or substitutedor unsubstituted heteroaryl.
 30. The compound of claim 29, wherein X isO.
 31. The compound of claim 29, wherein X is S.
 32. The compound ofclaim 29, wherein m is
 1. 33. The compound of claim 29, wherein R₂′ issubstituted or unsubstituted heteroaryl.
 34. The compound of claim 23,wherein R₂ is selected from one of the following:


35. The compound of claim 23, wherein R₂ is selected from one of thefollowing:


36. The compound of claim 23, wherein R₂ is

wherein X is N, and Y is NH, S, or O.
 37. The compound of claim 23,wherein R₂ is


38. The compound of claim 23, wherein R₃ is a substituted orunsubstituted aryl.
 39. The compound of claim 23, wherein R₃ is anunsubstituted phenyl moiety.
 40. The compound of claim 23, wherein R₃ isa substituted phenyl moiety.
 41. The compound of claim 23 of theformula:

wherein n is an integer between 1 and 5, inclusive; and each occurrenceof R₃′ is independently hydrogen; halogen; cyclic or acyclic,substituted or unsubstituted, branched or unbranched aliphatic; cyclicor acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(C); —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C);—SO₂R_(C); —NO₂; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein eachoccurrence of R_(C) is independently a hydrogen, a protecting group, analiphatic moiety, a heteroaliphatic moiety, an acyl moiety; an arylmoiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio;amino, alkylamino, dialkylamino, heteroaryloxy; or heteroarylthiomoiety.
 42. The compound of claim 23 of the formula:


43. The compound of claim 23 of one of the formulae:


44. (canceled)
 45. A compound of formula:

wherein each occurrence of R₁ is independently cyclic or acyclic,substituted or unsubstituted, branched or unbranched aliphatic; cyclicor acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; substituted or unsubstituted, branched or unbranchedacyl; substituted or unsubstituted, branched or unbranched aryl;substituted or unsubstituted, branched or unbranched heteroaryl;—OR_(A); —C(═O)R_(A); —CO₂R_(A); —SR_(A); —SOR_(A); —SO₂R_(A);—N(R_(A))₂; —NHC(O)R_(A); or —C(R_(A))₃; wherein each occurrence ofR_(A) is independently a hydrogen, a protecting group, an aliphaticmoiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; aheteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino,alkylamino, dialkylamino, heteroaryloxy; or heteroarylthio moiety; R₂ ishydrogen; halogen; cyclic or acyclic, substituted or unsubstituted,branched or unbranched aliphatic; cyclic or acyclic, substituted orunsubstituted, branched or unbranched heteroaliphatic; substituted orunsubstituted, branched or unbranched acyl; substituted orunsubstituted, branched or unbranched aryl; substituted orunsubstituted, branched or unbranched heteroaryl; —OR_(B); —C(═O)R_(B);—CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N(R_(B))₂;—NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) isindependently a hydrogen, a protecting group, an aliphatic moiety, aheteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroarylmoiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,dialkylamino, heteroaryloxy; or heteroarylthio moiety; andpharmaceutically acceptable salts and derivatives thereof.
 46. Apharmaceutical composition comprising a compound of claim 1 and apharmaceutically acceptable excipient. 47-50. (canceled)
 51. A method ofinhibiting histone deacetylase, the method comprising steps of:contacting a histone deacetylase with a compound of claim
 1. 52-54.(canceled)
 55. A method of inhibiting tubulin deacetylase, the methodcomprising steps of: contacting a tubulin deacetylase with a compound ofclaim
 1. 56. A method of inhibiting an aggresome, the method comprisingsteps of: contacting a aggresome with a compound of claim
 1. 57. Amethod of treating a subject with a proliferative disorder, the methodcomprising steps of: administering a therapeutically effective amount ofa compound of claim 1 to a subject. 58-61. (canceled)
 62. A method oftreating a subject with a protein degradation disorder, the methodcomprising steps of: administering a therapeutically effective amount ofa compound of claim 1 to a subject. 63-68. (canceled)
 69. A method ofpreparing a compound of formula

the method comprising steps of: providing an epoxy alcohol of formula:

reacting the epoxy alcohol with a reagent having the structure R_(B)XHunder suitable conditions to generate a diol of formula:

reducing the nitro group to generate a diol of formula:

reacting the amino group with acylating agent to generate a diol offormula:

reacting the diol with a reagent having the structure R₃CH(OMe)₂, orother acetal under suitable conditions to generate a 1,3-dioxane offormula:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone deacetylase as described herein;R_(B) is hydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety; X is—O—, —C(R′)₂—, —S—, or —NR′—, wherein R′ is hydrogen, a protectinggroup, or an aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic or heteroaromatic moiety; and R³ is an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety.
 70. Amethod of preparing a compound of formula

the method comprising steps of: providing an epoxy alcohol of formula:

reacting the epoxy alcohol with a reagent having the structure R_(B)XHunder suitable conditions to generate a diol of formula:

reducing the nitro group to generate a diol of formula:

reacting the amino group with acylating agent to generate a diol offormula:

reacting the diol with an aldehyde of formula R₃CHO under suitableconditions to generate a 1,3-dioxane of formula:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone deacetylase as described herein;R_(B) is hydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety; X is—O—, —C(R′)₂—, —S—, or —NR′—, wherein R′ is hydrogen, a protectinggroup, or an aliphatic, alicyclic, heteroaliphatic, heterocyclic,aromatic or heteroaromatic moiety; and R³ is an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic, or heteroaromatic moiety.
 71. Amethod of synthesizing a compound of

the method comprising steps of: providing an beta-hydroxy ketone offormula:

reducing the ketone to generate a diol of formula:

reducing the nitro group to generate a diol of formula:

reacting the amino group with acylating agent to generate a diol offormula:

reacting the diol with a reagent having the structure R₂CH(OMe)₂ orother acetal under suitable conditions to generate a compound offormula:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone or tubulin deacetylase asdescribed herein; R_(B) is hydrogen, a protecting group, or analiphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic, orheteroaromatic moiety; X is —O—, —C(R′)₂—, —S—, or —NR′—, wherein R′ ishydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic or heteroaromatic moiety; and R³is an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic, orheteroaromatic moiety.
 72. A method of synthesizing a compound of

the method comprising steps of: providing an beta-hydroxy ketone offormula:

reducing the ketone to generate a diol of formula:

reducing the nitro group to generate a diol of formula:

reacting the amino group with acylating agent to generate a diol offormula:

reacting the diol with an aldehyde of formula R₂CHO under suitableconditions to generate a compound of formula:

wherein R₁′ is -L-A, wherein L is a linker moiety; and A comprises afunctional group that inhibits histone or tubulin deacetylase asdescribed herein; R_(B) is hydrogen, a protecting group, or analiphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic, orheteroaromatic moiety; X is —O—, —C(R′)₂—, —S—, or —NR′—, wherein R′ ishydrogen, a protecting group, or an aliphatic, alicyclic,heteroaliphatic, heterocyclic, aromatic or heteroaromatic moiety; and R³is an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic, orheteroaromatic moiety. 73-76. (canceled)